diff --git a/MANIFEST.in b/MANIFEST.in index cb190f2..7e9dd3d 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -6,6 +6,5 @@ include SigProfilerAssignment/data/Reference_Signatures/GRCh38/* include SigProfilerAssignment/data/Reference_Signatures/mm9/* include SigProfilerAssignment/data/Reference_Signatures/mm10/* include SigProfilerAssignment/data/Reference_Signatures/rn6/* -include SigProfilerAssignment/src/FormatFiles/* -include SigProfilerAssignment/src/Fonts/* -include SigProfilerAssignment/src/* \ No newline at end of file +include SigProfilerAssignment/DecompositionPlots/reference_files/Fonts/* +include SigProfilerAssignment/DecompositionPlots/reference_files/* \ No newline at end of file diff --git a/README.md b/README.md index a1ea131..0302395 100644 --- a/README.md +++ b/README.md @@ -3,7 +3,7 @@ -drawing +drawing # SigProfilerAssignment SigProfilerAssignment is a new mutational attribution and decomposition tool that performs the following functions: @@ -72,7 +72,7 @@ spa_analyze( samples, output, signatures=None, signature_database=None,decompo ``` --> ### Decompose Fit Decomposes the De Novo Signatures into COSMIC Signatures and assigns COSMIC signatures into samples. -drawing +drawing ```python from SigProfilerAssignment import Analyzer as Analyze @@ -86,9 +86,12 @@ Analyze.decompose_fit(samples, exclude_signature_subgroups=exclude_signature_subgroups, exome=False) ``` + +## Analysis + ### *De Novo* Fit Attributes mutations of given Samples to input denovo signatures. -drawing +drawing ```python from SigProfilerAssignment import Analyzer as Analyze @@ -102,7 +105,7 @@ Analyze.denovo_fit( samples, ### COSMIC Fit Attributes mutations of given Samples to input COSMIC signatures. Note that penalties associated with denovo fit and COSMIC fits are different. -drawing +drawing ```python from SigProfilerAssignment import Analyzer as Analyze @@ -121,9 +124,10 @@ Analyze.cosmic_fit( samples, ## Main Parameters | Parameter | Variable Type | Parameter Description | | --------------------- | -------- |-------- | -| **samples** | String | Path to a tab delimilted file that contains the samples table where the rows are mutation types and colunms are sample IDs. or Path to VCF files directory if input files are VCF Files. | +| **samples** | String | Path to input file for `input_type`: Path to input folder for `input_type`:| | **output** | String | Path to the output folder. | - | **input_type** | String | The type of input:
Default value is "matrix"| + | **input_type** | String | The type of input:
The default value is "matrix".| +| **context_type**| String| Required context type if `input_type` is "vcf". `context_type` takes which context type of the input data is considered for assignment. Valid options include "96", "288", "1536", "DINUC", and "INDEL". The default value is "96".| | **signatures** | String | Path to a tab delimited file that contains the signature table where the rows are mutation types and colunms are signature IDs. | | **genome_build** | String | The reference genome build. List of supported genomes: "GRCh37", "GRCh38", "mm9", "mm10" and "rn6". The default value is "GRCh37". If the selected genome is not in the supported list, the default genome will be used. | | **cosmic_version** | Float | Takes a positive float among 1, 2, 3, 3.1, 3.2 and 3.3. Defines the version of the COSMIC reference signatures. The default value is 3.3. | @@ -131,13 +135,14 @@ Analyze.cosmic_fit( samples, | **make_plots** | Boolean | Toggle on and off for making and saving all plots. Default value is True. | | **exclude_signature_subgroups** | List | Removes the signatures corresponding to specific subtypes for better fitting. The usage is given above. Default value is None. | | **exome** | Boolean | Defines if the exome renormalized signatures will be used. The default value is False. | -| **context_type**| String| Reqd context type if "input_type" is "vcf". 'context_type' takes what context type of the mutation matrix to be considered for assignment. Valid options include '96', '6', '24', '4608', '288', '18','6144', '384', '1536', 'DINUC'. Default Value is '96'| | **verbose** | Boolean | Prints statements. Default value is False. | -#### SPA analysis Example for a matrix +## Examples + +### SPA analysis - Example for a matrix ```python @@ -167,7 +172,7 @@ Analyze.cosmic_fit( samples, ``` -#### SPA analysis Example for input vcf files +### SPA analysis - Example for input vcf files ```python @@ -198,6 +203,36 @@ Analyze.cosmic_fit( samples, exome=False) ``` + +### SPA analysis - Example for an input multi-sample segmentation file + + +```python +#import modules +import SigProfilerAssignment as spa +from SigProfilerAssignment import Analyzer as Analyze + +#set directories and paths to signatures and samples +dir_inp = spa.__path__[0]+'/data/Examples/' +samples = spa.__path__[0]+'/data/cnvtest/all.breast.ascat.summary.sample.tsv' # segmentation file +output = "output_example/" + +#Analysis of SP Assignment +Analyze.cosmic_fit( samples, + output, + input_type="seg:ASCAT_NGS", + context_type="CNV48", + signatures=None, + signature_database=None, + genome_build="GRCh37", + cosmic_version=3.3, + verbose=False, + collapse_to_SBS96=False, + make_plots=True, + exclude_signature_subgroups=None, + exome=False) +``` + ## Copyright This software and its documentation are copyright 2022 as a part of the SigProfiler project. The SigProfilerAssignment framework is free software and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py new file mode 100644 index 0000000..a58f65f --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition.py @@ -0,0 +1,341 @@ +#!/usr/bin/env python3 + +""" +Created: March 10th, 2020 +@author: Mark Barnes + +PlotDecomposition works with matrix formats SigProfiler SBS-96, SBS-1536, DBS-78, +and ID-83. This program is intended to take two matrices. + +(1) Sample matrix - A SigProfiler formatted SBS-96, SBS-1536, DBS-78, or ID-83 +matrix. +(2) Basis matrix - A SigProfiler formatted SBS-96, SBS-1536, DBS-78, or ID-83 +matrix that is the decomposition of (1). + +When running the function 'run_PlotDecomposition' a plot of the decomposition will +be generated and saved to the output folder. Refer to the function below to learn +more about the parameters required to generate the decomposition plot. +""" + +import os +import pandas as pd +import numpy as np +import scipy.stats +import sigProfilerPlotting as pltCNV +from SigProfilerAssignment.DecompositionPlots import SigProfilerPlottingMatrix as sigPlt +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_SBS96 as spd_96 +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_SBS288 as spd_288 +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_SBS1536 as spd_1536 +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_DBS78 as spd_78 +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_ID83 as spd_83 +from SigProfilerAssignment.DecompositionPlots import PlotDecomposition_CNV48 as cnv_48 +from SigProfilerAssignment import decompose_subroutines as sub +# imports for working with plots in memory +import io +from PIL import Image +from reportlab.lib.utils import ImageReader +# Global Variables +SBS_CONTEXTS = ["6", "24", "96", "288", "384", "1536", "6144"] +DBS_CONTEXTS = ["78", "186", "1248", "2976"] +ID_CONTEXTS = ["28", "83", "415"] +CNV_CONTEXTS = ["48"] +mtype_options = ["6", "24", "96", "384", "1536", "6144", "28", "83", "415", "78", "186", "1248", "2976"] + +# Helper function for converting BytesIO to image so it can be plotted by reportlab +def bytes_to_img(byte_png): + byte_png.seek(0) + tmp_im=Image.open(byte_png) + image = ImageReader(tmp_im) + return image + +# Helper function to convert byte array to image array +def open_byte_to_img_dict(byte_dict): + img_dict = dict() + for name in byte_dict.keys(): + tmp_img = bytes_to_img(byte_dict[name]) + img_dict[name] = tmp_img + return img_dict + + + +def calculate_similarities(denovo, denovo_name, est_denovo): + from numpy import inf + + # If matrix is 1536 context, then collapse it to 96 format + if denovo.shape[0]==1536: + index = denovo.iloc[:,0] + denovo_tmp = pd.DataFrame(denovo, index=index) + denovo_tmp = denovo.groupby(denovo_tmp.index.str[1:8]).sum() + denovo = pd.DataFrame(denovo_tmp) + denovo = denovo.reset_index() + elif denovo.shape[0]==288: + index = denovo.iloc[:,0] + denovo_tmp = pd.DataFrame(denovo, index=index) + denovo_tmp = denovo.groupby(denovo_tmp.index.str[2:9]).sum() + denovo = pd.DataFrame(denovo_tmp) + denovo = denovo.reset_index() + + + sample_names = [denovo_name] + + if sample_names is False: + sample_names = ["None"]*denovo.shape[1] + + cosine_similarity_list = [] + cosine_distance_list = [] + correlation_list = [] + correlation_distance_list = [] + kl_divergence_list = [] + l1_norm_list = [] + l2_norm_list = [] + relative_l1_list = [] + relative_l2_list = [] + + p_i = denovo[denovo_name] + q_i = est_denovo + + cosine_similarity_list.append(round(sub.cos_sim(p_i,q_i ),3)) + cosine_distance_list.append(round(scipy.spatial.distance.cosine(p_i, q_i),3)) + correlation_list.append(round(scipy.stats.pearsonr(p_i,q_i)[0],3)) + correlation_distance_list.append(round(1-scipy.stats.pearsonr(p_i,q_i)[0],3)) + kl_divergence_list.append(round(scipy.stats.entropy(p_i,q_i),4)) + l1_norm_list.append(round(np.linalg.norm(p_i-q_i , ord=1),2)) + relative_l1_list.append(round((l1_norm_list[-1]/np.linalg.norm(p_i, ord=1))*100,3)) + l2_norm_list.append(round(np.linalg.norm(p_i-q_i , ord=2),2)) + relative_l2_list.append(round((l2_norm_list[-1]/np.linalg.norm(p_i, ord=2))*100,3)) + kl_divergence_list = np.array(kl_divergence_list) + kl_divergence_list[kl_divergence_list == inf] =1000 + + similarities_dataframe = pd.DataFrame({"Sample Names": sample_names, \ + "Cosine Similarity": cosine_similarity_list, \ + "Cosine Distance": cosine_distance_list, \ + "Correlation Distance": correlation_distance_list, \ + "Correlation Coefficient": correlation_list, \ + "L1 Norm": l1_norm_list, \ + "L1 Norm %":relative_l1_list, \ + "L2 Norm": l2_norm_list, \ + "L2 Norm %": relative_l2_list, \ + "KL Divergence": kl_divergence_list}) + similarities_dataframe = similarities_dataframe.set_index("Sample Names") + + return similarities_dataframe + + +def genSBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype): + denovo_plots = dict() + basis_plots = dict() + if mtype == "1536" or mtype == "288": + denovo_plots = sigPlt.plotSBS(denovo_mtx, output_path, project, mtype, True) + basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, "96", True) + elif mtype == "96": + denovo_plots = sigPlt.plotSBS(denovo_mtx, output_path, project, mtype, True) + basis_plots = sigPlt.plotSBS(basis_mtx, output_path, project, mtype, True) + return denovo_plots,basis_plots + +def genDBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype): + denovo_plots = dict() + basis_plots = dict() + denovo_plots = sigPlt.plotDBS(denovo_mtx, output_path, project, mtype, True) + basis_plots = sigPlt.plotDBS(basis_mtx, output_path, project, mtype, True) + return denovo_plots,basis_plots + +def genID_pngs(denovo_mtx, basis_mtx, output_path, project, mtype): + denovo_plots = dict() + basis_plots = dict() + denovo_plots = sigPlt.plotID(denovo_mtx, output_path, project, mtype, True) + basis_plots = sigPlt.plotID(basis_mtx, output_path, project, mtype, True) + return denovo_plots,basis_plots + +def genCNV_pngs(denovo_mtx, basis_mtx, output_path, project, mtype): + denovo_plots = dict() + basis_plots = dict() + denovo_plots = pltCNV.plotCNV(denovo_mtx, output_path, project, plot_type="pdf", percentage=True, aggregate=False, read_from_file=False, write_to_file=False) + basis_plots = pltCNV.plotCNV(basis_mtx, output_path, project, plot_type="pdf", percentage=True, aggregate=False, read_from_file=False, write_to_file=False) + return denovo_plots,basis_plots + +# signames, weights +def gen_sub_plots(denovo_mtx, basis_mtx, output_path, project, mtype): + + if mtype in SBS_CONTEXTS: + if not os.path.exists(output_path): + os.makedirs(output_path) + denovo_plots,basis_plots=genSBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype) + return denovo_plots,basis_plots + elif mtype in DBS_CONTEXTS: + if not os.path.exists(output_path): + os.makedirs(output_path) + denovo_plots,basis_plots=genDBS_pngs(denovo_mtx, basis_mtx, output_path, project, mtype) + return denovo_plots,basis_plots + elif mtype in ID_CONTEXTS: + if not os.path.exists(output_path): + os.makedirs(output_path) + denovo_plots,basis_plots=genID_pngs(denovo_mtx, basis_mtx, output_path, project, mtype) + return denovo_plots,basis_plots + elif mtype in CNV_CONTEXTS: + if not os.path.exists(output_path): + os.makedirs(output_path) + denovo_plots, basis_plots=genCNV_pngs(denovo_mtx, basis_mtx, output_path, project, mtype) + return denovo_plots,basis_plots + else: + print("ERROR: mtype is " + mtype + " and is not yet supported.") + +# generate the plot for the reconstruction +def gen_reconstructed_png(denovo_name, basis_mtx, basis_names, weights, output_path, project, mtype): + reconstruction_plot=dict() + col_names=[denovo_name] + mut_col = basis_mtx.iloc[:,0] + + recon_plot = basis_mtx[basis_names[0]]*float(weights[0].strip("%"))/100 + + for i in range(1,len(weights)): + recon_plot = recon_plot + basis_mtx[basis_names[i]]*(float(weights[i].strip("%"))/100) + + recon_plot = pd.Series(recon_plot, name=denovo_name) + reconstruction_mtx = pd.concat([mut_col, recon_plot], axis=1) + if mtype in SBS_CONTEXTS: + if mtype == "1536" or mtype == "288": + reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx, output_path, "reconstruction_" + project, "96", True) + else: + reconstruction_plot=sigPlt.plotSBS(reconstruction_mtx, output_path, "reconstruction_" + project, mtype, True) + elif mtype in DBS_CONTEXTS: + reconstruction_plot=sigPlt.plotDBS(reconstruction_mtx, output_path, "reconstruction_" + project, mtype, True) + elif mtype in ID_CONTEXTS: + reconstruction_plot=sigPlt.plotID(reconstruction_mtx, output_path, "reconstruction_" + project, mtype, True) + elif mtype in CNV_CONTEXTS: + reconstruction_plot = pltCNV.plotCNV(reconstruction_mtx, output_path, "reconstruction_"+project, plot_type="pdf", \ + percentage=True, aggregate=False, read_from_file=False, write_to_file=False) + else: + print("ERROR: mtype is " + mtype + " and is not yet supported.") + + return reconstruction_mtx,reconstruction_plot + + +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + mtype, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction=False, statistics=None, sig_version=None, custom_text=None): + + """ + Generate the correct plot based on mtype. + + Parameters: + ---------- + denovo_name: (String) Name of denovo signature + basis_names: (List of Strings) Names of basis signatures + weights: (List of Strings) Percentile contribution for each basis signature + output_path: (String) Path to existing output directory + project: (String) Project name appended to file names + mtype: (String) The context 'mtype_options' has valid values + denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values + basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values + reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values + reconstruction: (Boolean) True to generate plot w/ reconstruction + statistics: (Pandas Dataframe) Output from calculate_similarities() + """ + + if mtype == "6": + print("Need to add support for SBS6 Decomposition") + elif mtype == "24": + print("Need to add support for SBS24 Decomposition") + elif mtype == "96": + byte_plot=spd_96.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + elif mtype == "288": + byte_plot=spd_288.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + elif mtype == "384": + print("Need to add support for SBS24 Decomposition") + elif mtype == "1536": + byte_plot=spd_1536.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + elif mtype == "6144": + print("Need to add support for SBS6144 Decomposition") + elif mtype == "28": + print("Need to add support for ID28 Decomposition") + elif mtype == "83": + byte_plot=spd_83.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + elif mtype == "415": + print("Need to add support for ID415 Decomposition") + elif mtype == "78": + byte_plot=spd_78.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + elif mtype == "186": + print("Need to add support for DBS186 Decomposition") + elif mtype == "1248": + print("Need to add support for DBS1248 Decomposition") + elif mtype == "2976": + print("Need to add support for DBS2976 Decomposition") + elif mtype == "48": + byte_plot=cnv_48.gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version, custom_text) + return byte_plot + + + +def run_PlotDecomposition(denovo_mtx, denovo_name, basis_mtx, basis_names, \ + weights, nonzero_exposures, output_path, project, mtype, sig_version=None, custom_text=None): + """ + Generates a decomposition plot of the denovo_mtx using the basis_mtx. + + Parameters: + ---------- + + denovo_mtx: Pandas Dataframe. This format represents the catalog of mutations seperated by tab. + + denovo_name: String. The name of the one sample in denovo_mtx to decompose. + + basis_mtx: Pandas Dataframe. This format represents the catalog of mutations seperated by tab. + + basis_names: List of Strings. The names of the samples in denovo_mtx that + the denovo_name sample from denovo_mtx is decomposed into. + ie. basis_names=["SBS1", "SBS5", "SBS15", "SBS20"] + + weights: List of Strings. The percentile weight corresponding to each basis + in basis_names. Refer to example function call below for more detail. + ie. weights=["11.58%", "42.38%", "16.46%", "29.58%"] + + output_path: String. Path to where to store the output. + + project: String. This string is appended to the file name output. + + mtype: String. The context of the data. Valid values include: "96", "1536","78", and "83". + + sig_version: String. The version of signatures being used. + + custom_text: String. A custom message displayed on decomposition plot. + + Returns: + ------- + None. + """ + + denovo_plots_dict,basis_plots_dict=gen_sub_plots(denovo_mtx, basis_mtx, output_path, project, mtype) + reconstructed_mtx,reconstruction_plot_dict = gen_reconstructed_png(denovo_name, basis_mtx, basis_names, \ + weights, output_path, project, mtype) + + present_sigs=np.array(basis_mtx[basis_names]) + reconstructed_mtx = np.dot(present_sigs,nonzero_exposures) + + denovo_plots_dict = open_byte_to_img_dict(denovo_plots_dict) + basis_plots_dict = open_byte_to_img_dict(basis_plots_dict) + reconstruction_plot_dict = open_byte_to_img_dict(reconstruction_plot_dict) + + statistics=calculate_similarities(denovo_mtx, denovo_name, reconstructed_mtx) + byte_plot = gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + mtype, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction=True, statistics=statistics, sig_version=sig_version, \ + custom_text=custom_text) + + + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py new file mode 100644 index 0000000..c4398a6 --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_CNV48.py @@ -0,0 +1,381 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape, portrait +from reportlab.lib import utils +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER PORTRAIT DIMENSIONS +WIDTH_LETTER = 965 +HEIGHT_LETTER = 755 +MID_WIDTH_LETTER = WIDTH_LETTER/2 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +# CNV48 plots have a dimension of 16" width, 10" height +WIDTH_GRAPH = 290 +HEIGHT_GRAPH = 214.89 + +# Layout Formatting +HEIGHT_GAP = 26 +WIDTH_GAP = 6 + +# For indexing the layout variables +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 55.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) + +LAYOUT_6_GRAPH = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH/2), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-564.56 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-564.56 - HEIGHT_GRAPH/2)] +LAYOUT_6_TEXT = [ +(600, 700), +(900, 700), +(600, 480), +(900, 480), +(600, 260), +(900, 260)] + +LAYOUT_5_GRAPH = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH/2), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-564.56 - HEIGHT_GRAPH/2)] +LAYOUT_5_TEXT = [ +(600, 700), +(900, 700), +(600, 480), +(900, 480), +(600, 260)] + +LAYOUT_4_GRAPH = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-349.6 - HEIGHT_GRAPH), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-349.6 - HEIGHT_GRAPH)] +LAYOUT_4_TEXT = [ +(600, 700 - HEIGHT_GRAPH/2), +(900, 700 - HEIGHT_GRAPH/2), +(600, 480 - HEIGHT_GRAPH/2), +(900, 480 - HEIGHT_GRAPH/2)] + +LAYOUT_3_GRAPH = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-124.78 - HEIGHT_GRAPH), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-349.6 - HEIGHT_GRAPH)] +LAYOUT_3_TEXT = [ +(600, 700 - HEIGHT_GRAPH/2), +(900, 700 - HEIGHT_GRAPH/2), +(600, 480 - HEIGHT_GRAPH/2-4.9)] + + +LAYOUT_2_GRAPH = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2), +(784 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2)] +LAYOUT_2_TEXT = [ +(600, 480), +(900, 480)] + +LAYOUT_2_GRAPH_RECON = [ +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-265.055-74.61), +(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-489.945-74.61)] +LAYOUT_2_TEXT_RECON = [ +(600, 700 - HEIGHT_GRAPH/2), +(600, 480 - HEIGHT_GRAPH/2-4.9)] + + +LAYOUT_1_GRAPH = [(485 - WIDTH_GRAPH/2, HEIGHT_LETTER-344.67 - HEIGHT_GRAPH/2)] +LAYOUT_1_TEXT = [(600, 480)] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8) + 32.75, HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER-564.64, 439.785), +(HEIGHT_LETTER-564.64, 439.785), +(HEIGHT_LETTER-564.64, 439.785), +(HEIGHT_LETTER-672, 654.67)] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,6): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_6_GRAPH[i][X_COORD], LAYOUT_6_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_6_TEXT[i][X_COORD], LAYOUT_6_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_7_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,6): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_6_GRAPH[i][X_COORD], LAYOUT_6_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_6_TEXT[i][X_COORD], LAYOUT_6_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(6, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD - 330, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) + 557, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + cos_sim = statistics["Cosine Similarity"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT_RECON[1][Y_COORD]-195, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT_RECON[1][Y_COORD]-205, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT_RECON[1][Y_COORD]-195, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT_RECON[1][Y_COORD]-205, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT_RECON[1][Y_COORD]-195, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT_RECON[1][Y_COORD]-205, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(GRAPH_X_COORD - 330, LAYOUT_2_TEXT_RECON[1][Y_COORD]-205, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + paths = cosmic.__path__[0] + + num_plts = num_bases - 1 + + if(num_bases >= 5): + num_plts = 4 + + c_draw.drawImage(BRACKET_PATH, 310, BRACKET_SIZES[num_plts][0], width = 20, \ + height = BRACKET_SIZES[num_plts][1], mask='auto') + +# Helper function to remove the margins from the PlotDecomposition pdf +# Parameters: +# pdf_to_edit - (String) The path to the uncropped decomposition plot +# num_bases - (Integer) The number of signatures the sample is composed of +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + + if (num_bases == 1): + page.mediaBox.lowerRight = (935-WIDTH_GRAPH,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (935-WIDTH_GRAPH,640) + page.mediaBox.upperLeft = (0,640) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (935,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (935,640) + page.mediaBox.upperLeft = (0,640) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (935,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (935,640) + page.mediaBox.upperLeft = (0,640) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (935,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (935,640) + page.mediaBox.upperLeft = (0,640) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (935,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (935,745) + page.mediaBox.upperLeft = (0,745) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 6): + page.mediaBox.lowerRight = (935,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (935,745) + page.mediaBox.upperLeft = (0,745) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 6): + page.mediaBox.lowerRight = (935,35) + page.mediaBox.lowerLeft = (0,35) + page.mediaBox.upperRight = (935,745) + page.mediaBox.upperLeft = (0,745) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE, IT CHANGES + num_bases = len(bases) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 6): + plot_6(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 6): + plot_7_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, LAYOUT_2_GRAPH_RECON[0][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 25, LAYOUT_2_TEXT_RECON[0][Y_COORD], "Original") + c.drawImage(recon_image, WIDTH_GAP, LAYOUT_2_GRAPH_RECON[1][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 45, LAYOUT_2_TEXT_RECON[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,HEIGHT_LETTER-377.75 + 33) + p.lineTo(WIDTH_GRAPH + 2,HEIGHT_LETTER-377.75 + 33) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH/2, width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + draw_bracket(num_bases, c) + + c.showPage() + + +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, reconstruction, \ + statistics, sig_version=None, custom_text=None): + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=(WIDTH_LETTER, HEIGHT_LETTER)) + c.setFont("Arial-Bold", 5.24) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py new file mode 100644 index 0000000..3fcc1dc --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_DBS78.py @@ -0,0 +1,345 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape +from reportlab.lib import utils +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER LANDSCAPE DIMENSIONS +WIDTH_LETTER = 11 * inch +HEIGHT_LETTER = 8.5 * inch +MID_WIDTH_LETTER = 396 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +WIDTH_GRAPH = 375 +HEIGHT_GRAPH = 85 + +# Layout Formatting +HEIGHT_GAP = 93 +WIDTH_GAP = 6 +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 63.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) + +# Pairs are (x-coordinate, y-coordinate) +LAYOUT_5_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + +LAYOUT_5_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + + +LAYOUT_4_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) - HEIGHT_GRAPH/2 + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - HEIGHT_GRAPH/2 - 10)] + +LAYOUT_4_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1)- HEIGHT_GRAPH/2 + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4)- HEIGHT_GRAPH/2 - 10)] + + +LAYOUT_3_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + +LAYOUT_3_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + + +LAYOUT_2_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5)] + +LAYOUT_2_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5)] + + +LAYOUT_1_GRAPH = [(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUT_1_TEXT = [(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3))] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8), HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER * (2.5/8), HEIGHT_LETTER * (3/8)), +(HEIGHT_LETTER * (2/8), HEIGHT_LETTER * (4/8)), +(HEIGHT_LETTER * (1.5/8), HEIGHT_LETTER * (5/8)), +(HEIGHT_LETTER * (1/8), HEIGHT_LETTER * (6/8))] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(5, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) - 10, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + + cos_sim = statistics["Cosine Similarity"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-120, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + num_plts = num_bases - 1 + if(num_bases >= 5): + num_plts = 4 + c_draw.drawImage(BRACKET_PATH, MID_WIDTH_LETTER - 15, \ + BRACKET_SIZES[num_plts][0], width = 20, height = BRACKET_SIZES[num_plts][1], mask='auto') + +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + + if (num_bases == 1): + page.mediaBox.lowerRight = (792,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (792,402) + page.mediaBox.upperLeft = (0,402) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (792,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (792,422) + page.mediaBox.upperLeft = (0,422) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,462) + page.mediaBox.upperLeft = (0,462) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (792,112) + page.mediaBox.lowerLeft = (0,112) + page.mediaBox.upperRight = (792,498) + page.mediaBox.upperLeft = (0,498) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (792,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 5): + page.mediaBox.lowerRight = (792,50) + page.mediaBox.lowerLeft = (0,50) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE, IT CHANGES + num_bases = len(bases) + # print("num bases is: " + str(num_bases)) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 5): + plot_6_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, LAYOUT_2_GRAPH[0][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawImage(recon_image, WIDTH_GAP, LAYOUT_2_GRAPH[1][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 25, LAYOUT_2_TEXT[0][Y_COORD], "Original") + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 45, LAYOUT_2_TEXT[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,MID_HEIGHT_LETTER) + p.lineTo(WIDTH_GRAPH + 2,MID_HEIGHT_LETTER) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH/2, width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + draw_bracket(len(bases), c) + + c.showPage() + +# iterate over the csv file and generate plots accordingly +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, reconstruction, \ + statistics, sig_version=None, custom_text=None): + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=letter) + c.setPageSize(landscape(letter)) + c.setFont("Arial-Bold", 7.19) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py new file mode 100644 index 0000000..ff7bfd8 --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_ID83.py @@ -0,0 +1,353 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape +from reportlab.lib import utils +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER LANDSCAPE DIMENSIONS +WIDTH_LETTER = 11 * inch +HEIGHT_LETTER = 8.5 * inch +MID_WIDTH_LETTER = 396 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +WIDTH_GRAPH = 375 +HEIGHT_GRAPH = 95 + +# Layout Formatting +HEIGHT_GAP = 70 +WIDTH_GAP = 6 +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 40.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) + +# Pairs are (x-coordinate, y-coordinate) +LAYOUT_5_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + +LAYOUT_5_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1) + 40), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 35), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3) + 30), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) + 25), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 5) +20)] + + +LAYOUT_4_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) - HEIGHT_GRAPH/2 + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - HEIGHT_GRAPH/2 - 10)] + +LAYOUT_4_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1)- 7), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- 12), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- 22), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4)- 27)] + + +LAYOUT_3_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER + (HEIGHT_GRAPH/2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER - (HEIGHT_GRAPH/2)), +(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER - (HEIGHT_GRAPH/2 * 3) - 5)] + +LAYOUT_3_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 37), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3) + 32), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) + 27)] + + +LAYOUT_2_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER + 5), +(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH - 5)] + +LAYOUT_2_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)-11), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)-21)] + + +LAYOUT_1_GRAPH = [(GRAPH_X_COORD - WIDTH_GAP, MID_HEIGHT_LETTER - (HEIGHT_GRAPH/2))] + +LAYOUT_1_TEXT = [(TEXT_X_COORD, MID_HEIGHT_LETTER + (HEIGHT_GRAPH/4) - 1)] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8), HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER * (2.5/8), HEIGHT_LETTER * (3/8)), +(HEIGHT_LETTER * (2/8), HEIGHT_LETTER * (4/8)), +(HEIGHT_LETTER * (1.5/8), HEIGHT_LETTER * (5/8)), +(HEIGHT_LETTER * (1/8), HEIGHT_LETTER * (6/8))] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(5, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) + 30, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + cos_sim = statistics["Cosine Similarity"][0] + cos_dist = statistics["Cosine Distance"][0] + cor_dist = statistics["Correlation Distance"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-120, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + num_plts = num_bases - 1 + if(num_bases >= 5): + num_plts = 4 + c_draw.drawImage(BRACKET_PATH, MID_WIDTH_LETTER - 15, \ + BRACKET_SIZES[num_plts][0], width = 15, \ + height = BRACKET_SIZES[num_plts][1], mask='auto') + +# Helper function to remove the margins from the PlotDecomposition pdf +# Parameters: +# pdf_to_edit - (String) The path to the uncropped decomposition plot +# output_name - (String) The name to save the cropped output as +# num_bases - (Integer) The number of signatures the sample is composed of +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + + if (num_bases == 1): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,407) + page.mediaBox.upperLeft = (0,407) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,422) + page.mediaBox.upperLeft = (0,422) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,460) + page.mediaBox.upperLeft = (0,460) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (792,105) + page.mediaBox.lowerLeft = (0,105) + page.mediaBox.upperRight = (792,505) + page.mediaBox.upperLeft = (0,505) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (792,55) + page.mediaBox.lowerLeft = (0,55) + page.mediaBox.upperRight = (792,555) + page.mediaBox.upperLeft = (0,555) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 5): + page.mediaBox.lowerRight = (792,35) + page.mediaBox.lowerLeft = (0,35) + page.mediaBox.upperRight = (792,555) + page.mediaBox.upperLeft = (0,555) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE, IT CHANGES + num_bases = len(bases) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 5): + plot_6_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, LAYOUT_2_GRAPH[0][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawImage(recon_image, WIDTH_GAP, LAYOUT_2_GRAPH[1][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 35, LAYOUT_2_TEXT[0][Y_COORD], "Original") + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 55, LAYOUT_2_TEXT[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,MID_HEIGHT_LETTER) + p.lineTo(WIDTH_GRAPH + 2,MID_HEIGHT_LETTER) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH/2, width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + + + draw_bracket(len(bases), c) + + c.showPage() + +# iterate over the csv file and generate plots accordingly +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, reconstruction, \ + statistics, sig_version=None, custom_text=None): + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=letter) + c.setPageSize(landscape(letter)) + c.setFont("Arial-Bold", 7.19) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py new file mode 100644 index 0000000..f80551d --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS1536.py @@ -0,0 +1,352 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape +from reportlab.platypus import Image +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER LANDSCAPE DIMENSIONS +WIDTH_LETTER = 11 * inch +HEIGHT_LETTER = 8.5 * inch +MID_WIDTH_LETTER = 396 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +WIDTH_GRAPH = 375 +HEIGHT_GRAPH = 85 + +# Layout Formatting +HEIGHT_GAP = 93 +WIDTH_GAP = 6 +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 63.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) + +# Pairs are (x-coordinate, y-coordinate) +LAYOUT_5_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + +LAYOUT_5_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + + +LAYOUT_4_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) - HEIGHT_GRAPH/2 + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - HEIGHT_GRAPH/2 - 10)] + +LAYOUT_4_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1)- HEIGHT_GRAPH/2 + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4)- HEIGHT_GRAPH/2 - 10)] + + +LAYOUT_3_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + +LAYOUT_3_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + + +LAYOUT_2_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5)] + +LAYOUT_2_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5)] + + +LAYOUT_1_GRAPH = [(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUT_1_TEXT = [(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3))] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8), HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER * (2.5/8), HEIGHT_LETTER * (3/8)), +(HEIGHT_LETTER * (2/8), HEIGHT_LETTER * (4/8)), +(HEIGHT_LETTER * (1.5/8), HEIGHT_LETTER * (5/8)), +(HEIGHT_LETTER * (1/8), HEIGHT_LETTER * (6/8))] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(5, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) - 10, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + cos_sim = statistics["Cosine Similarity"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-120, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + num_plts = num_bases - 1 + if(num_bases >= 5): + num_plts = 4 + + c_draw.drawImage(BRACKET_PATH, MID_WIDTH_LETTER - 15, \ + BRACKET_SIZES[num_plts][0], width = 20, height = BRACKET_SIZES[num_plts][1], \ + mask='auto') + +# Helper function to remove the margins from the PlotDecomposition pdf +# Parameters: +# pdf_to_edit - (String) The path to the uncropped decomposition plot +# output_name - (String) The name to save the cropped output as +# num_bases - (Integer) The number of signatures the sample is composed of +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + if (num_bases == 1): + page.mediaBox.lowerRight = (792,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (792,512) + page.mediaBox.upperLeft = (0,512) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (792,155) + page.mediaBox.lowerLeft = (0,155) + page.mediaBox.upperRight = (792,512) + page.mediaBox.upperLeft = (0,512) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,512) + page.mediaBox.upperLeft = (0,512) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (792,110) + page.mediaBox.lowerLeft = (0,110) + page.mediaBox.upperRight = (792,512) + page.mediaBox.upperLeft = (0,512) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (792,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 5): + page.mediaBox.lowerRight = (792,50) + page.mediaBox.lowerLeft = (0,50) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE + num_bases = len(bases) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 5): + plot_6_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER, width=WIDTH_GRAPH, height=HEIGHT_GRAPH*2.4) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 38, LAYOUT_2_TEXT[1][Y_COORD]+205, "Original") + c.drawImage(recon_image, WIDTH_GAP,(GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5, \ + width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 45, LAYOUT_2_TEXT[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,MID_HEIGHT_LETTER) + p.lineTo(WIDTH_GRAPH + 2,MID_HEIGHT_LETTER) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(output_path+"/SBS_sub_plots/"+de_novo+"_"+project+".png", \ + WIDTH_GAP, MID_HEIGHT_LETTER - (HEIGHT_GRAPH), width=WIDTH_GRAPH, \ + height=HEIGHT_GRAPH * 2.4) + draw_bracket(len(bases), c) + # save page + c.showPage() + +# iterate over the csv file and generate plots accordingly +def gen_decomposition(denovo_name, basis_names, weights, output_path, \ + project, denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, \ + reconstruction, statistics, sig_version=None, custom_text=None): + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=letter) + c.setPageSize(landscape(letter)) + c.setFont("Arial-Bold", 7.19) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py new file mode 100644 index 0000000..8ee9ec4 --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS288.py @@ -0,0 +1,360 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape +from reportlab.lib import utils +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER LANDSCAPE DIMENSIONS +WIDTH_LETTER = 11 * inch +HEIGHT_LETTER = 8.5 * inch +MID_WIDTH_LETTER = 396 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +WIDTH_GRAPH = 375 +HEIGHT_GRAPH = 85 + +# Layout Formatting +HEIGHT_GAP = 93 +WIDTH_GAP = 6 +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 63.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) +#print(pdfmetrics.sorted_list()) + +# Pairs are (x-coordinate, y-coordinate) +LAYOUT_5_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + +LAYOUT_5_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + + +LAYOUT_4_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) - HEIGHT_GRAPH/2 + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - HEIGHT_GRAPH/2 - 10)] + +LAYOUT_4_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1)- HEIGHT_GRAPH/2 + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4)- HEIGHT_GRAPH/2 - 10)] + + +LAYOUT_3_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + +LAYOUT_3_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + + +LAYOUT_2_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5)] + +LAYOUT_2_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5)] + + +LAYOUT_1_GRAPH = [(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUT_1_TEXT = [(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUTS = [(LAYOUT_1_GRAPH,LAYOUT_1_TEXT), (LAYOUT_2_GRAPH, LAYOUT_2_TEXT), +(LAYOUT_3_GRAPH,LAYOUT_3_TEXT),(LAYOUT_4_GRAPH, LAYOUT_4_TEXT), (LAYOUT_5_GRAPH, LAYOUT_5_TEXT)] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8), HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER * (2.5/8), HEIGHT_LETTER * (3/8)), +(HEIGHT_LETTER * (2/8), HEIGHT_LETTER * (4/8)), +(HEIGHT_LETTER * (1.5/8), HEIGHT_LETTER * (5/8)), +(HEIGHT_LETTER * (1/8), HEIGHT_LETTER * (6/8))] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(5, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) - 10, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + cos_sim = statistics["Cosine Similarity"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-120, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + paths = cosmic.__path__[0] + + num_plts = num_bases - 1 + + if(num_bases >= 5): + num_plts = 4 + + c_draw.drawImage(BRACKET_PATH, MID_WIDTH_LETTER - 15, \ + BRACKET_SIZES[num_plts][0], width = 20, \ + height = BRACKET_SIZES[num_plts][1], mask='auto') + +# Helper function to remove the margins from the PlotDecomposition pdf +# Parameters: +# pdf_to_edit - (String) The path to the uncropped decomposition plot +# output_name - (String) The name to save the cropped output as +# num_bases - (Integer) The number of signatures the sample is composed of +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + + if (num_bases == 1): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,402) + page.mediaBox.upperLeft = (0,402) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,422) + page.mediaBox.upperLeft = (0,422) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,462) + page.mediaBox.upperLeft = (0,462) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (792,112) + page.mediaBox.lowerLeft = (0,112) + page.mediaBox.upperRight = (792,498) + page.mediaBox.upperLeft = (0,498) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (792,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 5): + page.mediaBox.lowerRight = (792,55) + page.mediaBox.lowerLeft = (0,55) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE, IT CHANGES + num_bases = len(bases) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 5): + plot_6_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, LAYOUT_2_GRAPH[0][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 25, LAYOUT_2_TEXT[0][Y_COORD] + 15, "Original") + c.drawImage(recon_image, WIDTH_GAP, LAYOUT_2_GRAPH[1][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 45, LAYOUT_2_TEXT[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,MID_HEIGHT_LETTER) + p.lineTo(WIDTH_GRAPH + 2,MID_HEIGHT_LETTER) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH/2, width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + draw_bracket(num_bases, c) + + + c.showPage() + + +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, reconstruction, \ + statistics, sig_version=None, custom_text=None): + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=letter) + c.setPageSize(landscape(letter)) + c.setFont("Arial-Bold", 7.19) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py new file mode 100644 index 0000000..968c20f --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/PlotDecomposition_SBS96.py @@ -0,0 +1,358 @@ +#!/usr/bin/env python3 +""" +Created: February 21, 2020 +@author: Mark Barnes +""" +import reportlab +import os +from reportlab.pdfgen import canvas +from reportlab.lib.pagesizes import letter, A4, landscape +from reportlab.lib import utils +from reportlab.pdfbase.ttfonts import TTFont +from reportlab.pdfbase import pdfmetrics +import SigProfilerAssignment as spa_path +from PyPDF2 import PdfFileWriter, PdfFileReader, PdfFileMerger +# imports for saving plots to memory +import io +from PIL import Image +# imports for dashed line +from reportlab.lib.colors import black +paths = spa_path.__path__[0] +# Page Formatting +inch = 72 +# USING LETTER LANDSCAPE DIMENSIONS +WIDTH_LETTER = 11 * inch +HEIGHT_LETTER = 8.5 * inch +MID_WIDTH_LETTER = 396 +MID_HEIGHT_LETTER = HEIGHT_LETTER/2 + +WIDTH_GRAPH = 375 +HEIGHT_GRAPH = 85 + +# Layout Formatting +HEIGHT_GAP = 93 +WIDTH_GAP = 6 +X_COORD = 0 +Y_COORD = 1 + +# Coordinates for graphs on right side of plot +GRAPH_X_COORD = (WIDTH_LETTER) - WIDTH_GRAPH +GRAPH_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) +TEXT_X_COORD = GRAPH_X_COORD + WIDTH_GRAPH - 50 +TEXT_Y_COORD = (HEIGHT_LETTER - HEIGHT_GAP) + 63.75 + +FONTS_DIR = os.path.join(paths+'decomposition_plots/reference_files/Fonts/') +BRACKET_PATH=os.path.join(paths+"/decomposition_plots/reference_files/Accolade_fermante.png") +reportlab.rl_config.TTFSearchPath.append(FONTS_DIR) +pdfmetrics.registerFont(TTFont('Arial-Bold', 'Arial Bold.ttf')) + +# Pairs are (x-coordinate, y-coordinate) +LAYOUT_5_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + +LAYOUT_5_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1) + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 5) - 10)] + + +LAYOUT_4_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 1) - HEIGHT_GRAPH/2 + 10), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - HEIGHT_GRAPH/2 - 10)] + +LAYOUT_4_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 1)- HEIGHT_GRAPH/2 + 10), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4)- HEIGHT_GRAPH/2 - 10)] + + +LAYOUT_3_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3)), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + +LAYOUT_3_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2) + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 4) - 5)] + + +LAYOUT_2_GRAPH = [ +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 2) - HEIGHT_GRAPH/2 + 5), +(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3) - HEIGHT_GRAPH/2 - 5)] + +LAYOUT_2_TEXT = [ +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 2)- HEIGHT_GRAPH/2 + 5), +(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3)- HEIGHT_GRAPH/2 - 5)] + + +LAYOUT_1_GRAPH = [(GRAPH_X_COORD - WIDTH_GAP, (GRAPH_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUT_1_TEXT = [(TEXT_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 3))] + +LAYOUTS = [(LAYOUT_1_GRAPH,LAYOUT_1_TEXT), (LAYOUT_2_GRAPH, LAYOUT_2_TEXT), +(LAYOUT_3_GRAPH,LAYOUT_3_TEXT),(LAYOUT_4_GRAPH, LAYOUT_4_TEXT), (LAYOUT_5_GRAPH, LAYOUT_5_TEXT)] + +# Pairs (position, height), organized from 1 plot to 5 plus plots +BRACKET_SIZES = [ +(HEIGHT_LETTER * (3/8), HEIGHT_LETTER * (2/8)), +(HEIGHT_LETTER * (2.5/8), HEIGHT_LETTER * (3/8)), +(HEIGHT_LETTER * (2/8), HEIGHT_LETTER * (4/8)), +(HEIGHT_LETTER * (1.5/8), HEIGHT_LETTER * (5/8)), +(HEIGHT_LETTER * (1/8), HEIGHT_LETTER * (6/8))] + +PLOT_NAME = 0 +CONTRIBUTION = 1 + +# Helper functions for plotting the layout of a graph with 1-5 basis signatures +# Parameters: +# bases - (List of Strings) The list of basis names +# output_path - (String) The path to where the .png files are stored. +# project - (String) The name of the project that is post-fixed to each file name. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def plot_1(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + + for i in range(0,1): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_1_GRAPH[i][X_COORD], LAYOUT_1_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_1_TEXT[i][X_COORD], LAYOUT_1_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_2(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,2): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_2_GRAPH[i][X_COORD], LAYOUT_2_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_2_TEXT[i][X_COORD], LAYOUT_2_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_3(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + + for i in range(0,3): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_3_GRAPH[i][X_COORD], LAYOUT_3_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_3_TEXT[i][X_COORD], LAYOUT_3_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_4(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,4): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_4_GRAPH[i][X_COORD], LAYOUT_4_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_4_TEXT[i][X_COORD], LAYOUT_4_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_5(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + +def plot_6_plus(bases, project, c_draw, denovo_plots_dict, basis_plots_dict): + for i in range(0,5): + image=basis_plots_dict[bases[i][0]] + c_draw.drawImage(image, LAYOUT_5_GRAPH[i][X_COORD], LAYOUT_5_GRAPH[i][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c_draw.drawString(LAYOUT_5_TEXT[i][X_COORD], LAYOUT_5_TEXT[i][Y_COORD], str(bases[i][1]) + "%") + + extra_sigs = "* " + for i in range(5, len(bases)-1): + extra_sigs += str(bases[i][0]) + " (" + str(bases[i][1]) + "%), " + + extra_sigs += bases[len(bases)-1][0] + " (" + str(bases[len(bases)-1][1]) + "%)" + c_draw.drawString(GRAPH_X_COORD, (TEXT_Y_COORD - HEIGHT_GRAPH * 6) - 10, extra_sigs) + +# Helper function to add calculations to layout +# Parameters: +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +# statistics - (Pandas Dataframe) Dataframe w/ calculations +def draw_statistics(c_draw, statistics, sig_version, custom_text): + cos_sim = statistics["Cosine Similarity"][0] + cor_coeff = statistics["Correlation Coefficient"][0] + l1_norm_percent = statistics["L1 Norm %"][0] + l2_norm_percent = statistics["L2 Norm %"][0] + kl_divergence = statistics["KL Divergence"][0] + + + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "Cosine Similarity: " + str(cos_sim)) + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Correlation: " + str(cor_coeff)) + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "L1 Error %: " + str(l1_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+105, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "L2 Error %: " + str(l2_norm_percent) + "%") + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-90, \ + "KL Divergence: " + str(kl_divergence)) + + if sig_version is not None: + c_draw.drawString(WIDTH_GAP+195, LAYOUT_2_TEXT[1][Y_COORD]-100, \ + "Signature Version: " + str(sig_version)) + if custom_text is not None: + c_draw.drawString(WIDTH_GAP+15, LAYOUT_2_TEXT[1][Y_COORD]-120, \ + str(custom_text)) + +# Helper function to resize bracket depending on number of bases plotted +# Parameters: +# num_bases - (Integer) The number of bases to be plotted. +# c_draw - (Canvas) The canvas to draw the graph decomposition on. +def draw_bracket(num_bases, c_draw): + paths = cosmic.__path__[0] + + num_plts = num_bases - 1 + + if(num_bases >= 5): + num_plts = 4 + + c_draw.drawImage(BRACKET_PATH, MID_WIDTH_LETTER - 15, \ + BRACKET_SIZES[num_plts][0], width = 20, \ + height = BRACKET_SIZES[num_plts][1], mask='auto') + +# Helper function to remove the margins from the PlotDecomposition pdf +# Parameters: +# pdf_to_edit - (String) The path to the uncropped decomposition plot +# num_bases - (Integer) The number of signatures the sample is composed of +def crop_margins(pdf_to_edit, num_bases): + pdf_to_edit.seek(0) + pdf_file = PdfFileReader(pdf_to_edit, "rb") + page = pdf_file.getPage(0) + writer = PdfFileWriter() + output_plot_buff = io.BytesIO() + + if (num_bases == 1): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,402) + page.mediaBox.upperLeft = (0,402) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 2): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,422) + page.mediaBox.upperLeft = (0,422) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 3): + page.mediaBox.lowerRight = (792,150) + page.mediaBox.lowerLeft = (0,150) + page.mediaBox.upperRight = (792,462) + page.mediaBox.upperLeft = (0,462) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 4): + page.mediaBox.lowerRight = (792,112) + page.mediaBox.lowerLeft = (0,112) + page.mediaBox.upperRight = (792,498) + page.mediaBox.upperLeft = (0,498) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases == 5): + page.mediaBox.lowerRight = (792,75) + page.mediaBox.lowerLeft = (0,75) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + elif (num_bases > 5): + page.mediaBox.lowerRight = (792,55) + page.mediaBox.lowerLeft = (0,55) + page.mediaBox.upperRight = (792,537) + page.mediaBox.upperLeft = (0,537) + writer.addPage(page) + writer.write(output_plot_buff) + return output_plot_buff + +# Parameters: +# de_novo_name (String) The name of the denovo signature. +# basis_names (List of Strings) The names of the basis signatures +# output_path (String) Path to where to save the output. +# project (String) The project name that is appended to file names. +# c (Canvas) The canvas that is being drawn on. +# reconstruction (Boolean) True to create reconstruction +# statistics (Pandas Dataframe) If reconstructing, then include statistics. +# sig_version (String) The version of the Cosmic Signatures used +# denovo_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# basis_plots_dict (Dictionary) Signatures are keys, ByteIO plots are values +# reconstruction_plot_dict (Dictionary) Signatures are keys, ByteIO plots are values +# +# Output: +# A graph of the de_novo signature's decomposition. +def gen_plot(de_novo_name, bases, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict): + + # THIS IS THE RIGHT SIDE, IT CHANGES + num_bases = len(bases) + if (num_bases == 1): + plot_1(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 2): + plot_2(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 3): + plot_3(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 4): + plot_4(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases == 5): + plot_5(bases, project, c, denovo_plots_dict, basis_plots_dict) + elif (num_bases > 5): + plot_6_plus(bases, project, c, denovo_plots_dict, basis_plots_dict) + + recon_image=reconstruction_plot_dict[de_novo_name] + denovo_image=denovo_plots_dict[de_novo_name] + # THIS IS THE LEFT SIDE + if reconstruction: + c.drawImage(denovo_image, WIDTH_GAP, LAYOUT_2_GRAPH[0][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 25, LAYOUT_2_TEXT[0][Y_COORD], "Original") + c.drawImage(recon_image, WIDTH_GAP, LAYOUT_2_GRAPH[1][Y_COORD], width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + c.drawString(WIDTH_GRAPH - WIDTH_GAP - 45, LAYOUT_2_TEXT[1][Y_COORD], "Reconstructed") + draw_statistics(c, statistics, sig_version, custom_text) + + # Draw dashed line + c.setLineWidth(2) + c.setDash(25,5) + c.setStrokeColor(black) + c.setFillColorRGB(255,255,255) + p = c.beginPath() + p.moveTo(WIDTH_GAP,MID_HEIGHT_LETTER) + p.lineTo(WIDTH_GRAPH + 2,MID_HEIGHT_LETTER) + c.drawPath(p, stroke=1, fill=1) + else: + c.drawImage(denovo_image, WIDTH_GAP, MID_HEIGHT_LETTER - HEIGHT_GRAPH/2, width=WIDTH_GRAPH, height=HEIGHT_GRAPH) + draw_bracket(num_bases, c) + + + c.showPage() + + +def gen_decomposition(denovo_name, basis_names, weights, output_path, project, \ + denovo_plots_dict, basis_plots_dict, reconstruction_plot_dict, reconstruction, \ + statistics, sig_version=None, custom_text=None): + + + buff = io.BytesIO() + c = canvas.Canvas(buff, pagesize=letter) + c.setPageSize(landscape(letter)) + c.setFont("Arial-Bold", 7.19) + + basis_plots = [] + for i in range(0,len(basis_names)): + basis_plots.append([basis_names[i], weights[i]]) + + # create for loop to iterate through list, then change second value in list of lists + # Otherwise sorts strings and then 5.14% > 48.54% + for j in range(0, len(basis_names)): + basis_plots[j][1] = float(basis_plots[j][1].strip("%")) + sorted_list = sorted(basis_plots, key=lambda tup: tup[1], reverse=True) + + gen_plot(denovo_name, sorted_list, output_path, project, c, reconstruction, \ + statistics, sig_version, custom_text, denovo_plots_dict, basis_plots_dict, \ + reconstruction_plot_dict) + + c.save() + + # Take the plot and crop the margins + byte_plot = crop_margins(buff, len(basis_names)) + buff.close() + return byte_plot diff --git a/SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py b/SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py new file mode 100644 index 0000000..93e9beb --- /dev/null +++ b/SigProfilerAssignment/DecompositionPlots/SigProfilerPlottingMatrix.py @@ -0,0 +1,3479 @@ +#!/usr/bin/env python3 + +#Author: Erik Bergstrom + +# Modifications: +# SBS-96, SBS-1536, DBS-78, and ID-83 output to .png extension +# Input parameter matrix_path has been updated to be a pandas dataframe +# modifications made by Mark Barnes + +import matplotlib +matplotlib.use('Agg') +import matplotlib.pyplot as plt +import matplotlib.font_manager +from matplotlib.backends.backend_pdf import PdfPages +import matplotlib.patches as mplpatches +import re +import os +import sys +import argparse +from collections import OrderedDict +import pandas as pd +import numpy as np +# imports for saving plots to memory +import io +from PIL import Image + +def plotSBS(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None): + plot_custom_text = False + sig_probs = False + pcawg = False + buff_list = dict() + if plot_type == '96': + first_line=matrix_path.iloc[0,:] + if first_line[0][1] == ">": + pcawg = True + if first_line[0][5] != "]" and first_line[0][1] != ">": + sys.exit("The matrix does not match the correct SBS96 format. Please check you formatting and rerun this plotting function.") + + # pp = PdfPages(output_path + 'SBS_96_plots_' + project + '.pdf') + + mutations = OrderedDict() + total_count = [] + + if pcawg: + samples=matrix_path.columns[:] + samples = samples[2:] + else: + #samples = first_line.strip().split("\t") + samples=matrix_path.columns[:] + samples = samples[1:] + + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['C>A'] = OrderedDict() + mutations[sample]['C>G'] = OrderedDict() + mutations[sample]['C>T'] = OrderedDict() + mutations[sample]['T>A'] = OrderedDict() + mutations[sample]['T>C'] = OrderedDict() + mutations[sample]['T>G'] = OrderedDict() + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + #line = lines.strip().split(",") + mut_type = line[0] + nuc = line[1][0] + "[" + mut_type + "]" + line[1][2] + sample_index = 2 + else: + line = matrix_path.iloc[lines_tmp,:] + #line = lines.strip().split() + nuc = line[0] + mut_type = line[0][2:5] + sample_index = 1 + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + mutations[sample][mut_type][nuc] = mutCount + sample_index += 1 + + sample_count = 0 + for sample in mutations.keys(): + total_count = sum(sum(nuc.values()) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,9.92)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.04, 0.09, 0.95, 0.77]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + i = 0 + for key in mutations[sample]: + for seq in mutations[sample][key]: + xlabels.append(seq[0]+seq[2]+seq[6]) + if percentage: + if total_count > 0: + plt.bar(x, mutations[sample][key][seq]/total_count*100,width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq]/total_count*100 > ymax: + ymax = mutations[sample][key][seq]/total_count*100 + else: + plt.bar(x, mutations[sample][key][seq],width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq] > ymax: + ymax = mutations[sample][key][seq] + x += 1 + i += 1 + + x = .043 + y3 = .87 + y = int(ymax*1.25) + y2 = y+2 + for i in range(0, 6, 1): + panel1.add_patch(plt.Rectangle((x,y3), .15, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .159 + + yText = y3 + .06 + plt.text(.1, yText, 'C>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.255, yText, 'C>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.415, yText, 'C>T', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.575, yText, 'T>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.735, yText, 'T>C', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.89, yText, 'T>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + labs = np.arange(0.375,96.375,1) + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + panel1.set_xlim([0, 96]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + count = 0 + m = 0 + for i in range (0, 96, 1): + plt.text(i/101 + .0415, .02, xlabels[i][0], fontsize=30, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(i/101 + .0415, .044, xlabels[i][1], fontsize=30, color=colors[m], rotation='vertical', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(i/101 + .0415, .071, xlabels[i][2], fontsize=30, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + if count == 16: + count = 0 + m += 1 + + if sig_probs: + plt.text(0.045, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.045, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " subs", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_middle: + if len(custom_text_middle[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.98 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel1.text(x_pos_custom, 0.72, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel1.text(x_pos_custom, 0.68, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + + panel1.set_yticklabels(ylabels, fontsize=30) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.93,0.93,0.93], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + + if percentage: + plt.ylabel("Percentage of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=True, labelleft=True,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='lightgray', width=2) + + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + # Save matplot lib as a BytesIO, add to list, and return this list + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + + elif plot_type == '192' or plot_type == '96SB' or plot_type == '384': + first_line=matrix_path.iloc[0,:] + if first_line[0][6] == ">" or first_line[0][3] == ">": + pcawg = True + if first_line[0][7] != "]" and first_line[0][6] != ">" and first_line[0][3] != ">": + sys.exit("The matrix does not match the correct SBS192 format. Please check you formatting and rerun this plotting function.") + + mutations = OrderedDict() + + if pcawg: + samples=matrix_path.columns[:] + samples = samples[3:] + samples = [x.replace('"','') for x in samples] + else: + samples=matrix_path.columns[:] + samples = samples[1:] + + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['C>A'] = OrderedDict() + mutations[sample]['C>G'] = OrderedDict() + mutations[sample]['C>T'] = OrderedDict() + mutations[sample]['T>A'] = OrderedDict() + mutations[sample]['T>C'] = OrderedDict() + mutations[sample]['T>G'] = OrderedDict() + + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + line = [x.replace('"','') for x in line] + nuc = line[2][0] + "[" + line[1] + "]" + line[2][2] + bias = line[0][0] + else: + line = matrix_path.iloc[lines_tmp,:] + nuc = line[0][2:] + bias = line[0][0] + if bias == 'N' or bias == 'B': + continue + else: + if pcawg: + mut_type = line[1] + sample_index = 3 + else: + mut_type = line[0][4:7] + sample_index = 1 + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + if nuc not in mutations[sample][mut_type].keys(): + mutations[sample][mut_type][nuc] = [0,0] + if bias == 'T': + mutations[sample][mut_type][nuc][0] = mutCount + else: + mutations[sample][mut_type][nuc][1] = mutCount + sample_index += 1 + + sample_count = 0 + for sample in mutations.keys(): + total_count = sum(sum(sum(tsb) for tsb in nuc.values()) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,9.92)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.04, 0.09, 0.95, 0.77]) + xlabels = [] + + x = 0.7 + ymax = 0 + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + i = 0 + for key in mutations[sample]: + for seq in mutations[sample][key]: + xlabels.append(seq[0]+seq[2]+seq[6]) + if percentage: + if total_count > 0: + trans = plt.bar(x, mutations[sample][key][seq][0]/total_count*100,width=0.75,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.75 + untrans = plt.bar(x, mutations[sample][key][seq][1]/total_count*100,width=0.75,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + x += .2475 + if mutations[sample][key][seq][0]/total_count*100 > ymax: + ymax = mutations[sample][key][seq][0]/total_count*100 + if mutations[sample][key][seq][1]/total_count*100 > ymax: + ymax = mutations[sample][key][seq][1]/total_count*100 + + else: + trans = plt.bar(x, mutations[sample][key][seq][0],width=0.75,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.75 + untrans = plt.bar(x, mutations[sample][key][seq][1],width=0.75,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + x += .2475 + if mutations[sample][key][seq][0] > ymax: + ymax = mutations[sample][key][seq][0] + if mutations[sample][key][seq][1] > ymax: + ymax = mutations[sample][key][seq][1] + x += 1 + i += 1 + + x = .0415 + y3 = .87 + y = int(ymax*1.25) + x_plot = 0 + + + yText = y3 + .06 + plt.text(.1, yText, 'C>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.255, yText, 'C>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.415, yText, 'C>T', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.575, yText, 'T>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.735, yText, 'T>C', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.89, yText, 'T>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + + ytick_offest = int(y/4) + + for i in range(0, 6, 1): + panel1.add_patch(plt.Rectangle((x,y3), .155, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x_plot,0), 32, y, facecolor=colors[i], zorder=0, alpha = 0.25, edgecolor='grey')) + x += .1585 + x_plot += 32 + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + labs = np.arange(0.750,192.750,1) + + + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + panel1.set_xlim([0, 96]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + count = 0 + m = 0 + for i in range (0, 96, 1): + plt.text(i/101 + .0415, .02, xlabels[i][0], fontsize=30, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(i/101 + .0415, .044, xlabels[i][1], fontsize=30, color=colors[m], rotation='vertical', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(i/101 + .0415, .071, xlabels[i][2], fontsize=30, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + if count == 16: + count = 0 + m += 1 + + if sig_probs: + plt.text(0.045, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.045, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " transcribed subs", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_bottom: + if len(custom_text_bottom[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.84 + if custom_text_upper and custom_text_bottom: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_bottom: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_bottom: + panel1.text(x_pos_custom, 0.72, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_bottom: + custom_text_upper_plot = custom_text_bottom[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + + + panel1.set_yticklabels(ylabels, fontsize=30) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.6,0.6,0.6], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + plt.legend(handles=[trans, untrans], prop={'size':30}) + if percentage: + plt.ylabel("Percentage of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors=[0.6, 0.6, 0.6]) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + # IMPORTANT: SBS6 has yet to be updated + elif plot_type == '6': + with open(matrix_path) as f: + next(f) + first_line = f.readline() + first_line = first_line.strip().split() + if len(first_line[0]) > 3: + sys.exit("The matrix does not match the correct SBS6 format. Please check you formatting and rerun this plotting function.") + + pp = PdfPages(output_path + 'SBS_6_plots_' + project + '.pdf') + + mutations = OrderedDict() + total_count = [] + try: + with open (matrix_path) as f: + first_line = f.readline() + samples = first_line.strip().split("\t") + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['C>A'] = 0 + mutations[sample]['C>G'] = 0 + mutations[sample]['C>T'] = 0 + mutations[sample]['T>A'] = 0 + mutations[sample]['T>C'] = 0 + mutations[sample]['T>G'] = 0 + + for lines in f: + line = lines.strip().split() + nuc = line[0] + mut_type = line[0] + sample_index = 1 + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + mutations[sample][mut_type] = mutCount + sample_index += 1 + + for sample in mutations: + total_count = sum(mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(15,10)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.12, 0.12, 0.8, 0.77]) + xlabels = [] + + y = -0.5 + xmax = 0 + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + i = 0 + for key in mutations[sample]: + xlabels.append(key) + if percentage: + if total_count > 0: + plt.barh(y, mutations[sample][key]/total_count*100,height=0.7,color=colors[i],align='center', zorder=1000) + if mutations[sample][key]/total_count*100 > xmax: + xmax = mutations[sample][key]/total_count*100 + else: + plt.barh(y, mutations[sample][key],height=0.7,color=colors[i],align='center', zorder=1000) + if mutations[sample][key] > xmax: + xmax = mutations[sample][key] + y -= 1 + i += 1 + + y = .043 + x3 = .87 + x = int(xmax*1.1) + + + while x%4 != 0: + x += 1 + xtick_offest = int(x/4) + + if percentage: + xlabs = [0, round(xtick_offest, 1), round(xtick_offest*2, 1), round(xtick_offest*3, 1), round(xtick_offest*4, 1)] + xlabels= [str(0), str(round(xtick_offest, 1)) + "%", str(round(xtick_offest*2, 1)) + "%", + str(round(xtick_offest*3, 1)) + "%", str(round(xtick_offest*4, 1)) + "%"] + else: + xlabs = [0, xtick_offest, xtick_offest*2, xtick_offest*3, xtick_offest*4] + xlabels= [0, xtick_offest, xtick_offest*2, + xtick_offest*3, xtick_offest*4] + + # if not percentage: + # xlabels = ['{:,}'.format(int(x)) for x in xlabels] + + if not percentage: + xlabels = ['{:,}'.format(int(x)) for x in xlabels] + if len(xlabels[-1]) > 3: + xlabels_temp = [] + if len(xlabels[-1]) > 7: + for label in xlabels: + if len(label) > 7: + xlabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + + else: + for label in xlabels: + if len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + xlabels = xlabels_temp + + ylabs = np.arange(-5.5, 0.5, 1) + ylabels = (['T>G','T>C','T>A','C>T','C>G','C>A']) + panel1.set_xlim([0, x]) + panel1.set_ylim([-6, 0]) + panel1.set_xticks(xlabs) + panel1.set_yticks(ylabs) + panel1.set_xticklabels(xlabels, fontsize=30) + panel1.set_yticklabels(ylabels, fontsize=30) + panel1.spines['right'].set_visible(False) + panel1.spines['top'].set_visible(False) + + if sig_probs: + plt.text(.125, .9, sample, fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + else: + plt.text(.125, .9, sample + ": " + "{:,}".format(int(total_count)) + " subs", fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + + if percentage: + plt.xlabel("Percentage of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.xlabel("Number of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.set_ylabel('') + + panel1.tick_params(axis='both',which='both',\ + bottom=True, labelbottom=True,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + width=2) + + + + pp.savefig(plot1) + plt.close() + pp.close() + + except: + print("There may be an issue with the formatting of you matrix file.") + os.remove(output_path + 'SBS_6_plots_' + project + '.pdf') + # IMPORTANT: SBS24 has yet to be updated + elif plot_type == '12' or plot_type == '6SB' or plot_type == '24': + with open(matrix_path) as f: + next(f) + first_line = f.readline() + first_line = first_line.strip().split() + if first_line[0][1] != ":" or len(first_line[0]) != 5: + sys.exit("The matrix does not match the correct SBS192 format. Please check you formatting and rerun this plotting function.") + + pp = PdfPages(output_path + 'SBS_24_plots_' + project + '.pdf') + + mutations = OrderedDict() + + try: + with open (matrix_path) as f: + first_line = f.readline() + samples = first_line.strip().split("\t") + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['C>A'] = [0,0] + mutations[sample]['C>G'] = [0,0] + mutations[sample]['C>T'] = [0,0] + mutations[sample]['T>A'] = [0,0] + mutations[sample]['T>C'] = [0,0] + mutations[sample]['T>G'] = [0,0] + + for lines in f: + line = lines.strip().split() + nuc = line[0][2:] + bias = line[0][0] + if bias == 'N' or bias == 'B': + continue + else: + sample_index = 1 + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + if bias == 'T': + mutations[sample][nuc][0] = mutCount + else: + mutations[sample][nuc][1] = mutCount + sample_index += 1 + for sample in mutations: + total_count = sum(sum(tsb) for tsb in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(15,10)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.12, 0.12, 0.8, 0.77]) + + y = 12.485 + xmax = 0 + for key in mutations[sample]: + if percentage: + if total_count > 0: + trans = plt.barh(y, mutations[sample][key][0]/total_count*100,height=0.75,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + y -= 0.75 + untrans = plt.barh(y, mutations[sample][key][1]/total_count*100,height=0.75,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + y -= .2475 + if mutations[sample][key][0]/total_count*100 > xmax: + xmax = mutations[sample][key][0]/total_count*100 + if mutations[sample][key][1]/total_count*100 > xmax: + xmax = mutations[sample][key][1]/total_count*100 + + else: + trans = plt.barh(y, mutations[sample][key][0],height=0.75,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + y -= 0.75 + untrans = plt.barh(y, mutations[sample][key][1],height=0.75,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + y -= .2475 + if mutations[sample][key][0] > xmax: + xmax = mutations[sample][key][0] + if mutations[sample][key][1] > xmax: + xmax = mutations[sample][key][1] + y -= 1 + + x = int(xmax*1.1) + + while x%4 != 0: + x += 1 + + xtick_offest = int(x/4) + + + if percentage: + xlabs = [0, round(xtick_offest, 1), round(xtick_offest*2, 1), round(xtick_offest*3, 1), round(xtick_offest*4, 1)] + xlabels= [str(0), str(round(xtick_offest, 1)) + "%", str(round(xtick_offest*2, 1)) + "%", + str(round(xtick_offest*3, 1)) + "%", str(round(xtick_offest*4, 1)) + "%"] + else: + xlabs = [0, xtick_offest, xtick_offest*2, xtick_offest*3, xtick_offest*4] + xlabels= [0, xtick_offest, xtick_offest*2, + xtick_offest*3, xtick_offest*4] + if not percentage: + xlabels = ['{:,}'.format(int(x)) for x in xlabels] + if len(xlabels[-1]) > 3: + xlabels_temp = [] + if len(xlabels[-1]) > 7: + for label in xlabels: + if len(label) > 7: + xlabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + + else: + for label in xlabels: + if len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + xlabels = xlabels_temp + # if not percentage: + # xlabels = ['{:,}'.format(int(x)) for x in xlabels] + ylabs = np.arange(2.15, 13, 2) + ylabels = (['T>G','T>C','T>A','C>T','C>G','C>A']) + #labs = np.arange(0,12.485,) + panel1.set_xlim([0, x]) + panel1.set_ylim([1.2524, 13.235]) + panel1.set_yticks(ylabs) + panel1.set_xticks(xlabs) + panel1.set_xticklabels(xlabels, fontsize=30) + panel1.set_yticklabels(ylabels, fontsize=30) + panel1.set_xlabel('') + panel1.set_ylabel('') + panel1.spines['right'].set_visible(False) + panel1.spines['top'].set_visible(False) + + if sig_probs: + plt.text(.125, .9, sample, fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + else: + plt.text(.125, .9, sample + ": " + "{:,}".format(int(total_count)) + " transcribed subs", fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if percentage: + plt.xlabel("Percentage of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.xlabel("Number of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=True, labelbottom=True,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + width=2) + + plt.legend(handles=[trans, untrans], prop={'size':25}) + + pp.savefig(plot1) + plt.close() + pp.close() + + except: + print("There may be an issue with the formatting of you matrix file.") + os.remove(output_path + 'SBS_24_plots_' + project + '.pdf') + + elif plot_type == '288': + first_line=matrix_path.iloc[0,:] + if first_line[0][6] == ">" or first_line[0][3] == ">": + pcawg = True + if first_line[0][7] != "]" and first_line[0][6] != ">" and first_line[0][3] != ">": + sys.exit("The matrix does not match the correct SBS288 format. Please check you formatting and rerun this plotting function.") + + #pp = PdfPages(output_path + 'SBS_288_plots_' + project + '.pdf') + + mutations = OrderedDict() + mutations_TSB = OrderedDict() + total_count = [] + + if pcawg: + samples=matrix_path.columns[:] + samples = samples[2:] + else: + samples=matrix_path.columns[:] + samples = samples[1:] + + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['C>A'] = OrderedDict() + mutations[sample]['C>G'] = OrderedDict() + mutations[sample]['C>T'] = OrderedDict() + mutations[sample]['T>A'] = OrderedDict() + mutations[sample]['T>C'] = OrderedDict() + mutations[sample]['T>G'] = OrderedDict() + + mutations_TSB[sample] = OrderedDict() + mutations_TSB[sample]['All'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['C>A'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['C>G'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['C>T'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['T>A'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['T>C'] = OrderedDict({'T':0, 'U':0,'N':0}) + mutations_TSB[sample]['T>G'] = OrderedDict({'T':0, 'U':0,'N':0}) + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + mut_type = line[0] + nuc = line[1][0] + "[" + mut_type + "]" + line[1][2] + sample_index = 2 + else: + line = matrix_path.iloc[lines_tmp,:] + nuc = line[0] + mut_type = line[0][4:7] + sample_index = 1 + tsb = nuc[0] + + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + try: + mutCount = int(line[sample_index]) + except: + print("It appears that the provided matrix does not contain mutation counts.\n\tIf you have provided a signature activity matrix, please change the percentage parameter to True.\n\tOtherwise, ", end='') + if nuc[2:] not in mutations[sample][mut_type]: + mutations[sample][mut_type][nuc[2:]] = mutCount + else: + mutations[sample][mut_type][nuc[2:]] += mutCount + mutations_TSB[sample][mut_type][tsb] += mutCount + mutations_TSB[sample]['All'][tsb] += mutCount + sample_index += 1 + + sample_count = 0 + + for sample in mutations.keys(): + total_count = sum(sum(nuc.values()) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,9.92)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.04, 0.09, 0.7, 0.77]) + panel2 = plt.axes([0.77, 0.09, 0.21, 0.77]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + i = 0 + for key in mutations[sample]: + for seq in mutations[sample][key]: + xlabels.append(seq[0]+seq[2]+seq[6]) + if percentage: + if total_count > 0: + panel1.bar(x, mutations[sample][key][seq]/total_count*100,width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq]/total_count*100 > ymax: + ymax = mutations[sample][key][seq]/total_count*100 + else: + panel1.bar(x, mutations[sample][key][seq],width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq] > ymax: + ymax = mutations[sample][key][seq] + x += 1 + i += 1 + + x = .043 + y3 = .87 + y = int(ymax*1.25) + y2 = y+2 + for i in range(0, 6, 1): + panel1.add_patch(plt.Rectangle((x,y3), .11, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .117 + + yText = y3 + .06 + + + plt.text(.082, yText, 'C>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.1975, yText, 'C>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.315, yText, 'C>T', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.43, yText, 'T>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.55, yText, 'T>C', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.665, yText, 'T>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + y = ymax/1.025 + ytick_offest = float(y/3) + # ytick_offest = int(y/4) + + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + # ylabels= [str(0), str(round(ytick_offest)) + "%", str(round(ytick_offest*2)) + "%", + # str(round(ytick_offest*3)) + "%", str(round(ytick_offest*4)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + font_label_size = 30 + if not percentage: + if int(ylabels[3]) >= 1000: + font_label_size = 20 + + if percentage: + if len(ylabels) > 2: + font_label_size = 20 + + labs = np.arange(0.375,96.375,1) + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + panel1.set_xlim([0, 96]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + count = 0 + m = 0 + for i in range (0, 96, 1): + plt.text(i/137 + .04, .02, xlabels[i][0], fontsize=25, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(i/137 + .04, .044, xlabels[i][1], fontsize=25, color=colors[m], rotation='vertical', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(i/137 + .04, .071, xlabels[i][2], fontsize=25, color='gray', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + if count == 16: + count = 0 + m += 1 + + if sig_probs: + plt.text(0.045, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.045, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " subs", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_middle: + if len(custom_text_middle[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.73 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right',zorder=1) + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel1.text(x_pos_custom, 0.72, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel1.text(x_pos_custom, 0.68, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + + panel1.set_yticklabels(ylabels, fontsize=font_label_size) + panel1.yaxis.grid(True) + panel1.grid(which='major', axis='y', color=[0.93,0.93,0.93], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + + if percentage: + panel1.set_ylabel("Percentage of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + panel1.set_ylabel("Number of Single Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=True, labelleft=True,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='lightgray', width=2) + + + [i.set_color("black") for i in panel1.get_yticklabels()] + + + yp2 = 28 + labels = [] + y2max = 0 + tsbColors = [[1/256,70/256,102/256], [228/256,41/256,38/256], 'green'] + for mut in mutations_TSB[sample]: + labels.append(mut) + i = 0 + for tsb in mutations_TSB[sample][mut]: + if tsb == "T": + label = "Transcribed" + elif tsb == "U": + label = "Untranscribed" + else: + label = "Nontranscribed" + if percentage: + if total_count > 0: + panel2.barh(yp2, mutations_TSB[sample][mut][tsb]/total_count*100,color=tsbColors[i], label=label) + if mutations_TSB[sample][mut][tsb]/total_count*100 > y2max: + y2max = mutations_TSB[sample][mut][tsb]/total_count*100 + else: + if mutations_TSB[sample][mut][tsb] > y2max: + y2max = mutations_TSB[sample][mut][tsb] + + panel2.barh(yp2, mutations_TSB[sample][mut][tsb], color=tsbColors[i], label=label) + yp2 -= 1 + i += 1 + yp2 -=1 + + y = int(y2max*1.1) + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + if percentage: + xlabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + xlabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + xlabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + xlabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + + if not percentage: + xlabels = ['{:,}'.format(int(x)) for x in xlabels] + if len(xlabels[-1]) > 3: + xlabels_temp = [] + if len(xlabels[-1]) > 7: + for label in xlabels: + if len(label) > 7: + xlabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + + else: + for label in xlabels: + if len(label) > 3: + xlabels_temp.append(label[0:-4] + "k") + else: + xlabels_temp.append(label) + xlabels = xlabels_temp + panel2.spines['right'].set_visible(False) + panel2.spines['top'].set_visible(False) + labels.reverse() + panel2.set_yticks([3, 7, 11, 15, 19, 23, 27]) + panel2.set_yticklabels(labels, fontsize=30,fontname="Arial", weight = 'bold') + panel2.set_xticklabels(xlabels, fontsize=30) + panel2.set_xticks(xlabs) + handles, labels = panel2.get_legend_handles_labels() + panel2.legend(handles[:3], labels[:3], loc='best', prop={'size':30}) + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + +########################################################################################################################### + elif plot_type == '1536': + first_line=matrix_path.iloc[0,:] + if first_line[0][1] == '>': + pcawg = True + if first_line[0][6] != "]" and first_line[0][1] != '>': + sys.exit("The matrix does not match the correct SBS1536 format. Please check you formatting and rerun this plotting function.") + + mutations_96 = OrderedDict() + mutations = OrderedDict() + mutations_5 = OrderedDict() + mutations_3 = OrderedDict() + max_count = {} + max_all = {} + max_5 = {} + max_3 = {} + total_count = [] + total_counts = {'TT':0, 'TG':0,'TC':0,'TA':0, + 'GT':0,'GG':0,'GC':0,'GA':0, + 'CT':0,'CG':0,'CC':0,'CA':0, + 'AT':0,'AG':0,'AC':0,'AA':0,} + total_counts_5 = {'T':0, 'G':0,'C':0,'A':0} + total_counts_3 = {'T':0, 'G':0,'C':0,'A':0} + + first_line=matrix_path.iloc[0,:] + if pcawg: + samples=matrix_path.columns[:] + samples = samples[2:] + samples = [x.replace('"','') for x in samples] + else: + samples=matrix_path.columns[:] + samples = samples[1:] + + for sample in samples: + max_all[sample] = 0 + max_5[sample] = 0 + max_3[sample] = 0 + total_counts[sample]= {'TT':0, 'TG':0,'TC':0,'TA':0, + 'GT':0,'GG':0,'GC':0,'GA':0, + 'CT':0,'CG':0,'CC':0,'CA':0, + 'AT':0,'AG':0,'AC':0,'AA':0,} + total_counts_5[sample]= {'T':0, 'G':0,'C':0,'A':0} + total_counts_3[sample]= {'T':0, 'G':0,'C':0,'A':0} + + mutations_96[sample] = OrderedDict() + mutations_96[sample]['C>A'] = OrderedDict() + mutations_96[sample]['C>G'] = OrderedDict() + mutations_96[sample]['C>T'] = OrderedDict() + mutations_96[sample]['T>A'] = OrderedDict() + mutations_96[sample]['T>C'] = OrderedDict() + mutations_96[sample]['T>G'] = OrderedDict() + + max_count[sample] = 0 + mutations[sample] = OrderedDict() + mutations_5[sample] = OrderedDict() + mutations_3[sample] = OrderedDict() + + mutations[sample]['C>A'] = OrderedDict() + mutations_5[sample]['C>A'] = OrderedDict() + mutations_3[sample]['C>A'] = OrderedDict() + mutations[sample]['C>A'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['C>A'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['C>A'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + mutations[sample]['C>G'] = OrderedDict() + mutations_5[sample]['C>G'] = OrderedDict() + mutations_3[sample]['C>G'] = OrderedDict() + mutations[sample]['C>G'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['C>G'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['C>G'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + mutations[sample]['C>T'] = OrderedDict() + mutations_5[sample]['C>T'] = OrderedDict() + mutations_3[sample]['C>T'] = OrderedDict() + mutations[sample]['C>T'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['C>T'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['C>T'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + mutations[sample]['T>A'] = OrderedDict() + mutations_5[sample]['T>A'] = OrderedDict() + mutations_3[sample]['T>A'] = OrderedDict() + mutations[sample]['T>A'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['T>A'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['T>A'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + mutations[sample]['T>C'] = OrderedDict() + mutations_5[sample]['T>C'] = OrderedDict() + mutations_3[sample]['T>C'] = OrderedDict() + mutations[sample]['T>C'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['T>C'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['T>C'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + mutations[sample]['T>G'] = OrderedDict() + mutations_5[sample]['T>G'] = OrderedDict() + mutations_3[sample]['T>G'] = OrderedDict() + mutations[sample]['T>G'] = {'TT':OrderedDict(), 'TG':OrderedDict(), 'TC':OrderedDict(), 'TA':OrderedDict(), + 'GT':OrderedDict(), 'GG':OrderedDict(), 'GC':OrderedDict(), 'GA':OrderedDict(), + 'CT':OrderedDict(), 'CG':OrderedDict(), 'CC':OrderedDict(), 'CA':OrderedDict(), + 'AT':OrderedDict(), 'AG':OrderedDict(), 'AC':OrderedDict(), 'AA':OrderedDict()} + mutations_5[sample]['T>G'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + mutations_3[sample]['T>G'] = {'T':OrderedDict(),'G':OrderedDict(),'C':OrderedDict(),'A':OrderedDict()} + + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + line = [x.replace('"','') for x in line] + nuc = line[1][0:2] + "[" + line[0] + "]" + line[1][3:] + mut_type = line[0] + penta_key = line[1][0] + line[1][-1] + tri_key = line[1][1] + line[1][-2] + sample_index = 2 + else: + line = matrix_path.iloc[lines_tmp,:] + nuc = line[0] + mut_type = line[0][3:6] + penta_key = line[0][0] + line[0][-1] + tri_key = line[0][1] + line[0][-2] + sample_index = 1 + + tri = line[0][1:8] + + for sample in samples: + + if tri not in mutations_96[sample][mut_type]: + mutations_96[sample][mut_type][tri] = 0 + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + + if pcawg: + sample_ref = sample_index - 2 + else: + sample_ref = sample_index - 1 + if mutCount > max_count[samples[sample_ref]]: + max_count[samples[sample_ref]] = mutCount + + if mutCount > max_all[sample]: + max_all[sample] = mutCount + + mutations[sample][mut_type][penta_key][tri_key] = mutCount + total_counts[sample][penta_key] += mutCount + total_counts_5[sample][penta_key[0]] += mutCount + total_counts_3[sample][penta_key[1]] += mutCount + penta_key_short = penta_key[0] + mutations_5[sample][mut_type][penta_key_short][tri_key] = 0 + mutations_3[sample][mut_type][penta_key_short][tri_key] = 0 + mutations_96[sample][mut_type][tri] += mutCount + sample_index += 1 + + + sample_count = 0 + for sample in mutations.keys(): + total_count_sample = sum(sum(nuc.values()) for nuc in mutations_96[sample].values()) + total_count = max_all[sample]*1.1 + ratio = total_count/total_count_sample + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,22.5)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.03, 0.0677, 0.92, 0.267]) + panel2 = plt.axes([0.03, 0.65, 0.92, 0.267]) + panel3 = plt.axes([0.03, 0.35, 0.92, 0.1335]) # 3' context + panel4 = plt.axes([0.03, 0.5, 0.92, 0.1335]) # 5' context + xlabels = [] + ylabels = [] + ylabels_5 = [] + ylabels_3 = [] + + + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + colors_heat = [np.linspace(56/255,255/255,5), np.linspace(66/255,225/255,5), np.linspace(157/255,40/255,5)] + colors_heat_compact = [np.linspace(56/255,255/255,5), np.linspace(66/255,225/255,5), np.linspace(157/255,40/255,5)] + + + i = 0 + x_pos = 0 + x_inter = 0 + for key in mutations[sample]: + y_pos = 15 + for penta in mutations[sample][key]: + #total_count = total_counts[sample][penta] + key_5 = penta[0] + key_3 = penta[1] + ylabels.append(penta[0] + "---" + penta[1]) + for tri in mutations[sample][key][penta]: + tri_nuc = tri[0] + "[" + key + "]" + tri[1] + normalized = mutations_96[sample][key][tri_nuc] + try: + mut_count = int(int(20 * round(float(mutations[sample][key][penta][tri]/total_count_sample/ratio* 100))/20)/20) + mutations_5[sample][key][key_5][tri] += float(mutations[sample][key][penta][tri]) + mutations_3[sample][key][key_3][tri] += float(mutations[sample][key][penta][tri]) + if mutations_5[sample][key][key_5][tri] > max_5[sample]: + max_5[sample] = mutations_5[sample][key][key_5][tri] + if mutations_3[sample][key][key_3][tri] > max_3[sample]: + max_3[sample] = mutations_3[sample][key][key_3][tri] + + except: + mut_count = 0 + xlabels.append(tri[0]+"-"+tri[1]) + rectangle=mplpatches.Rectangle((x_pos, y_pos), 1, 1,\ + linewidth=1,\ + facecolor=(colors_heat[0][mut_count], colors_heat[1][mut_count], colors_heat[2][mut_count])) + + panel1.add_patch(rectangle) + x_pos += 1 + y_pos -= 1 + x_pos = x_inter + + x_inter += 17 + x_pos = x_inter + i += 1 + + + + x_pos = 0 + x_inter = 0 + total_count_5 = max_5[sample]*1.1 + total_count_3 = max_3[sample]*1.1 + ratio_5 = total_count_5/total_count_sample + ratio_3 = total_count_3/total_count_sample + ratio_total = max(ratio_5, ratio_3) + + for key in mutations_5[sample]: + y_pos = 3 + for penta in mutations_5[sample][key]: + # total_count_5 = total_counts_5[sample][penta] + # total_count_3 = total_counts_3[sample][penta] + + ylabels_5.append(penta + "---N" ) + ylabels_3.append("N---" + penta) + for tri in mutations_5[sample][key][penta]: + mut_count = int(int(20 * round(float(mutations_5[sample][key][penta][tri])/total_count_sample/ratio_total*100)/20)/20) + mut_count_3 = int(int(20 * round(float(mutations_3[sample][key][penta][tri])/total_count_sample/ratio_total*100)/20)/20) + rectangle=mplpatches.Rectangle((x_pos, y_pos), 1, 1,\ + linewidth=1,\ + facecolor=(colors_heat_compact[0][mut_count], colors_heat_compact[1][mut_count], colors_heat_compact[2][mut_count])) + + panel4.add_patch(rectangle) + rectangle=mplpatches.Rectangle((x_pos, y_pos), 1, 1,\ + linewidth=1,\ + facecolor=(colors_heat[0][mut_count_3], colors_heat[1][mut_count_3], colors_heat[2][mut_count_3])) + + panel3.add_patch(rectangle) + x_pos += 1 + y_pos -= 1 + x_pos = x_inter + x_inter += 17 + x_pos = x_inter + i += 1 + + x = 0.5 + ymax = 0 + colors = [[3/256,189/256,239/256], [1/256,1/256,1/256],[228/256,41/256,38/256], [203/256,202/256,202/256], [162/256,207/256,99/256], [236/256,199/256,197/256]] + i = 0 + + for key in mutations_96[sample]: + for seq in mutations_96[sample][key]: + xlabels.append(seq[0]+seq[2]+seq[6]) + if percentage: + if total_count_sample > 0: + panel2.bar(x, mutations_96[sample][key][seq]/total_count_sample*100,width=0.5,color=colors[i],align='center', zorder=1000) + if mutations_96[sample][key][seq]/total_count_sample*100 > ymax: + ymax = mutations_96[sample][key][seq]/total_count_sample*100 + else: + panel2.bar(x, mutations_96[sample][key][seq],width=0.5,color=colors[i],align='center', zorder=1000) + if mutations_96[sample][key][seq] > ymax: + ymax = mutations_96[sample][key][seq] + x += 1 + x += 1 + i += 1 + + + # scale bar for bottom 1536 plot + y_grad = .267/len(colors_heat[0]) + y_start = 0.0677 + for l in range (0, len(colors_heat[0]), 1): + rectangle=mplpatches.Rectangle((.96, y_start), .02, y_grad,\ + linewidth=1,\ + facecolor=(colors_heat[0][l], colors_heat[1][l], colors_heat[2][l]),\ + transform=plt.gcf().transFigure, clip_on=False,\ + edgecolor=(colors_heat[0][l], colors_heat[1][l], colors_heat[2][l])) + panel1.add_patch(rectangle) + y_start += y_grad + + # scale bar for top 1536 plot + y_grad = .1335/len(colors_heat_compact[0]) + y_start = 0.5 + for l in range (0, len(colors_heat_compact[0]), 1): + rectangle=mplpatches.Rectangle((.96, y_start), .02, y_grad,\ + linewidth=1,\ + facecolor=(colors_heat_compact[0][l], colors_heat_compact[1][l], colors_heat_compact[2][l]),\ + transform=plt.gcf().transFigure, clip_on=False,\ + edgecolor=(colors_heat_compact[0][l], colors_heat_compact[1][l], colors_heat_compact[2][l])) + panel1.add_patch(rectangle) + y_start += y_grad + + # scale bar for middle 1536 plot + y_grad = .1335/len(colors_heat_compact[0]) + y_start = 0.35 + for l in range (0, len(colors_heat_compact[0]), 1): + rectangle=mplpatches.Rectangle((.96, y_start), .02, y_grad,\ + linewidth=1,\ + facecolor=(colors_heat_compact[0][l], colors_heat_compact[1][l], colors_heat_compact[2][l]),\ + transform=plt.gcf().transFigure, clip_on=False,\ + edgecolor=(colors_heat_compact[0][l], colors_heat_compact[1][l], colors_heat_compact[2][l])) + panel1.add_patch(rectangle) + y_start += y_grad + y_tick_grad = max_count[sample]/2 + + # scale numbers for bottom 1536 plot + plt.text(.9825, .0677, '0', fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .2012, str(ratio/2)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .325, str(ratio)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + y = int(ymax*1.25) + + # scale numbers for top 1536 plot + plt.text(.9825, .5, '0', fontsize=20, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .56675, str(ratio_total/2)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .625, str(ratio_total)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + y = int(ymax*1.25) + + # scale numbers for middle 1536 plot + plt.text(.9825, .35, '0', fontsize=20, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .41675, str(ratio_total/2)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.9825, .475, str(ratio_total)[:5], fontsize=15, fontweight='bold', transform=plt.gcf().transFigure) + y = int(ymax*1.25) + + x = .033 + y3 = .92 + for i in range(0, 6, 1): + panel1.add_patch(plt.Rectangle((x,y3), .143, .03, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .154 + + + y3 = .9 + yText = y3 + 0.06 + plt.text(.085, yText, 'C>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.24, yText, 'C>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.395, yText, 'C>T', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.552, yText, 'T>A', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.705, yText, 'T>C', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.86, yText, 'T>G', fontsize=55, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + ylabels_96 = [] + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels_96= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels_96= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + font_label_size = 25 + if not percentage: + if int(ylabels_96[3]) >= 1000: + font_label_size = 20 + + + if not percentage: + ylabels_96 = ['{:,}'.format(int(x)) for x in ylabels_96] + if len(ylabels_96[-1]) > 3: + ylabels_temp = [] + if len(ylabels_96[-1]) > 7: + for label in ylabels_96: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels_96: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels_96 = ylabels_temp + + + panel1.set_xlim([0, 101]) + panel1.set_ylim([0, 16]) + panel2.set_xlim([0, 101]) + panel2.set_yticks(ylabs) + panel1.set_yticks([]) + panel1.set_xticks([]) + panel2.set_xticks([]) + panel4.set_xlim([0, 101]) + panel4.set_ylim([0, 4]) + panel3.set_xlim([0, 101]) + panel3.set_ylim([0, 4]) + panel4.set_yticks([]) + panel3.set_yticks([]) + panel3.set_xticks([]) + panel4.set_xticks([]) + + + + # x-axis 1536 bottom plot + m = 0 + count = 0 + x_letter = 0 + for i in range (0, 96, 1): + plt.text(x_letter/101 + .032, .04, xlabels[i][0], fontsize=25, color='black', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(x_letter/101 + .032, .05, xlabels[i][1], fontsize=25, color='black', rotation='vertical', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(x_letter/101 + .032, .06, xlabels[i][2], fontsize=25, color='black', rotation='vertical', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + x_letter += .92 + if (i+1)%16 == 0 and i != 0: + x_letter += .92 + if count == 16: + count = 0 + m += 1 + + # y-axis 1536 bottom plot + m = 0 + count = 0 + y_letter = 5.2 + for i in range (0, 16, 1): + plt.text(.003, y_letter/16 , ylabels[i][0], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(.008, y_letter/16 + 0, ylabels[i][1:4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(.022, y_letter/16 + 0, ylabels[i][4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + y_letter -= .2675 + + if count == 16: + count = 0 + m += 1 + + # y-axis 1536 top matrix plot + m = 0 + count = 0 + y_letter = 9.85 + for i in range (0, 4, 1): + plt.text(.003, y_letter/16 , ylabels_5[i][0], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(.008, y_letter/16 + 0, ylabels_5[i][1:4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(.022, y_letter/16 + 0, ylabels_5[i][4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + y_letter -= .53 + + if count == 16: + count = 0 + m += 1 + + # y-axis 1536 middle matrix plot + m = 0 + count = 0 + y_letter = 7.45 + for i in range (0, 4, 1): + plt.text(.003, y_letter/16 , ylabels_3[i][0], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + plt.text(.008, y_letter/16 + 0, ylabels_3[i][1:4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', fontweight='bold',transform=plt.gcf().transFigure) + plt.text(.022, y_letter/16 + 0, ylabels_3[i][4], fontsize=25, color='black', verticalalignment='center', fontname='Courier New', transform=plt.gcf().transFigure) + count += 1 + y_letter -= .53 + + if count == 16: + count = 0 + m += 1 + + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_middle: + if len(custom_text_middle[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.94 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel2.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel2.text(x_pos_custom, 0.86, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel2.text(x_pos_custom, 0.835, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel2.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + if sig_probs: + panel2.text(0.04, 0.875, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + panel2.text(0.04, 0.875, sample + ": " + "{:,}".format(int(total_count_sample)) + " subs", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + + panel2.grid(which='major', axis='y', color=[0.93,0.93,0.93], zorder=1) + panel2.set_yticklabels(ylabels_96, fontsize=font_label_size) + panel1.set_xlabel('') + panel1.set_ylabel('') + panel1.set_yticklabels([]) + panel1.set_xticklabels([]) + panel2.set_xticklabels([]) + + if percentage: + panel2.set_ylabel("Percentage of Single Base Substitutions", fontsize=25, fontname="Times New Roman", weight = 'bold') + else: + panel2.set_ylabel("Number of Single Base Substitutions", fontsize=25, fontname="Times New Roman", weight = 'bold') + + + panel1.axis('off') + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=False,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='white', width=2) + panel2.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=False,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='white', width=2) + panel3.axis('off') + panel3.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=False,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='white', width=2) + panel4.axis('off') + panel4.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=False,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='white', width=2) + + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + + else: + print("The provided plot_type: ", plot_type, " is not supported by this plotting function") + + +def plotID(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None): + # if 'roman' in matplotlib.font_manager.weight_dict: + # del matplotlib.font_manager.weight_dict['roman'] + # matplotlib.font_manager._rebuild() + plot_custom_text = False + sig_probs = False + pcawg = False + buff_list = dict() + if plot_type == '94' or plot_type == 'ID94' or plot_type == '94ID' or plot_type == '83': + first_line=matrix_path.iloc[0,:] + if first_line[0][1] == 'D' or first_line[0][0] == 'D': + pcawg = True + mutation_type = first_line[0] + mutation_type_list = mutation_type.split(":") + if len(mutation_type_list) != 4 and first_line[0][1] != 'D' and first_line[0][0] != 'D': + sys.exit("The matrix does not match the correct ID96 format. Please check you formatting and rerun this plotting function.") + #pp = PdfPages(output_path + 'ID_83_plots_' + project + '.pdf') + + indel_types = ['1:Del:C:0', '1:Del:C:1', '1:Del:C:2', '1:Del:C:3', '1:Del:C:4', '1:Del:C:5', + '1:Del:T:0', '1:Del:T:1', '1:Del:T:2', '1:Del:T:3', '1:Del:T:4', '1:Del:T:5', + '1:Ins:C:0', '1:Ins:C:1', '1:Ins:C:2', '1:Ins:C:3', '1:Ins:C:4', '1:Ins:C:5', + '1:Ins:T:0', '1:Ins:T:1', '1:Ins:T:2', '1:Ins:T:3', '1:Ins:T:4', '1:Ins:T:5', + # >1bp INDELS + '2:Del:R:0', '2:Del:R:1', '2:Del:R:2', '2:Del:R:3', '2:Del:R:4', '2:Del:R:5', + '3:Del:R:0', '3:Del:R:1', '3:Del:R:2', '3:Del:R:3', '3:Del:R:4', '3:Del:R:5', + '4:Del:R:0', '4:Del:R:1', '4:Del:R:2', '4:Del:R:3', '4:Del:R:4', '4:Del:R:5', + '5:Del:R:0', '5:Del:R:1', '5:Del:R:2', '5:Del:R:3', '5:Del:R:4', '5:Del:R:5', + '2:Ins:R:0', '2:Ins:R:1', '2:Ins:R:2', '2:Ins:R:3', '2:Ins:R:4', '2:Ins:R:5', + '3:Ins:R:0', '3:Ins:R:1', '3:Ins:R:2', '3:Ins:R:3', '3:Ins:R:4', '3:Ins:R:5', + '4:Ins:R:0', '4:Ins:R:1', '4:Ins:R:2', '4:Ins:R:3', '4:Ins:R:4', '4:Ins:R:5', + '5:Ins:R:0', '5:Ins:R:1', '5:Ins:R:2', '5:Ins:R:3', '5:Ins:R:4', '5:Ins:R:5', + #MicroHomology INDELS + '2:Del:M:1', '3:Del:M:1', '3:Del:M:2', '4:Del:M:1', '4:Del:M:2', '4:Del:M:3', + '5:Del:M:1', '5:Del:M:2', '5:Del:M:3', '5:Del:M:4', '5:Del:M:5'] + mutations = OrderedDict() + + first_line=matrix_path.iloc[0,:] + if pcawg: + samples=matrix_path.columns[:] + samples = samples[4:] + samples = [x.replace('"','') for x in samples] + else: + samples=matrix_path.columns[:] + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['1DelC'] = [0,0,0,0,0,0] + mutations[sample]['1DelT'] = [0,0,0,0,0,0] + mutations[sample]['1InsC'] = [0,0,0,0,0,0] + mutations[sample]['1InsT'] = [0,0,0,0,0,0] + mutations[sample]['2DelR'] = [0,0,0,0,0,0] + mutations[sample]['3DelR'] = [0,0,0,0,0,0] + mutations[sample]['4DelR'] = [0,0,0,0,0,0] + mutations[sample]['5DelR'] = [0,0,0,0,0,0] + mutations[sample]['2InsR'] = [0,0,0,0,0,0] + mutations[sample]['3InsR'] = [0,0,0,0,0,0] + mutations[sample]['3InsR'] = [0,0,0,0,0,0] + mutations[sample]['4InsR'] = [0,0,0,0,0,0] + mutations[sample]['5InsR'] = [0,0,0,0,0,0] + mutations[sample]['2DelM'] = [0] + mutations[sample]['3DelM'] = [0,0] + mutations[sample]['4DelM'] = [0,0,0] + mutations[sample]['5DelM'] = [0,0,0,0,0] + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + line = [x.replace('"','') for x in line] + if line[1] == 'repeats': + mut_type = line[2][0] + line[0][0] + line[0][1].lower() + line[0][2].lower() + "R" + else: + mut_type = line[2][0] + line[0][0] + line[0][1].lower() + line[0][2].lower() + line[1][0] + try: + repeat_size = int(line[3]) + except: + repeat_size = int(line[3][0]) + if line[1] == 'MH': + repeat_size -= 1 + sample_index = 4 + else: + line = matrix_path.iloc[lines_tmp,:] + if line[0] not in indel_types: + continue + categories = line[0].split(":") + mut_type = categories[0] + categories[1] + categories[2] + repeat_size = int(categories[3]) + if categories[2] == 'M': + repeat_size -= 1 + sample_index = 1 + + for sample in samples: + if mut_type in mutations[sample].keys(): + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + mutations[sample][mut_type][repeat_size] = mutCount + else: + continue + sample_index += 1 + + sample_count = 0 + for sample in mutations.keys(): + total_count = sum(sum(nuc) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,12)) + plt.rc('axes', edgecolor='black') + panel1 = plt.axes([0.045, 0.17, 0.92, 0.65]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[253/256,190/256,111/256], [255/256,128/256,2/256], [176/256,221/256,139/256], [54/256,161/256,46/256], + [253/256,202/256,181/256], [252/256,138/256,106/256], [241/256,68/256,50/256], [188/256,25/256,26/256], + [208/256,225/256,242/256], [148/256,196/256,223/256], [74/256,152/256,201/256], [23/256,100/256,171/256], + [226/256,226/256,239/256], [182/256,182/256,216/256], [134/256,131/256,189/256], [98/256,64/256,155/256]] + + i = 0 + for key in mutations[sample]: + l = 1 + for seq in mutations[sample][key]: + xlabels.append(l) + if percentage: + if total_count > 0: + plt.bar(x, seq/total_count*100,width=0.4,color=colors[i],align='center', zorder=1000) + if seq/total_count*100 > ymax: + ymax = seq/total_count*100 + else: + plt.bar(x, seq,width=0.4,color=colors[i],align='center', zorder=1000) + if seq > ymax: + ymax = seq + x += 1 + l += 1 + i += 1 + + x = .0475 + y_top = .827 + y_bottom = .114 + y = int(ymax*1.25) + y2 = y+2 + for i in range(0, 12, 1): + panel1.add_patch(plt.Rectangle((x,y_top), .0595, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .0595, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .0665 + + panel1.add_patch(plt.Rectangle((x-.001,y_top), .006, .05, facecolor=colors[12], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x-.001,y_bottom), .006, .05, facecolor=colors[12], clip_on=False, transform=plt.gcf().transFigure)) + x +=.011 + panel1.add_patch(plt.Rectangle((x,y_top), .0155, .05, facecolor=colors[13], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .0155, .05, facecolor=colors[13], clip_on=False, transform=plt.gcf().transFigure)) + x += .022 + panel1.add_patch(plt.Rectangle((x,y_top), .027, .05, facecolor=colors[14], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .027, .05, facecolor=colors[14], clip_on=False, transform=plt.gcf().transFigure)) + x += .0335 + panel1.add_patch(plt.Rectangle((x,y_top), .049, .05, facecolor=colors[15], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .049, .05, facecolor=colors[15], clip_on=False, transform=plt.gcf().transFigure)) + + + + + yText = y_top + .01 + plt.text(.072, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.1385, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + plt.text(.205, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.2715, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + plt.text(.338, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.4045, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.471, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.5375, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + plt.text(.604, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.6705, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.737, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.8035, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + plt.text(.844, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.861, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.888, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.93, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + + yText_labels_top = yText + .075 + yText_labels_bottom = y_bottom - .03 + yText_labels_bottom_sec = yText_labels_bottom - .045 + + plt.text(.08, yText_labels_top, '1bp Deletion', fontsize=40, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.21, yText_labels_top, '1bp Insertion', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.375, yText_labels_top, '>1bp Deletion at Repeats\n (Deletion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.64, yText_labels_top, '>1bp Insertions at Repeats\n (Insertion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.85, yText_labels_top, ' Mircohomology\n(Deletion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + plt.text(.058, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=35, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.19, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.39, yText_labels_bottom_sec, 'Number of Repeat Units', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.65, yText_labels_bottom_sec, 'Number of Repeat Units', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.85, yText_labels_bottom_sec, 'Mircohomology Length', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + x = .0477 + for i in range (0, 8, 1): + if i != 2 and i != 3: + plt.text(x, yText_labels_bottom, '1 2 3 4 5 6+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + else: + plt.text(x, yText_labels_bottom, '0 1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + x += .0665 + + for i in range (0, 4, 1): + plt.text(x, yText_labels_bottom, '0 1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .0665 + + plt.text(x, yText_labels_bottom, '1', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .011 + plt.text(x, yText_labels_bottom, '1 2', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .022 + plt.text(x, yText_labels_bottom, '1 2 3', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .0335 + plt.text(x, yText_labels_bottom, '1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + labs = np.arange(0.375,83.375,1) + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + panel1.set_xlim([0, 83]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + + if sig_probs: + plt.text(0.0475, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.0475, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " indels", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_middle: + if len(custom_text_middle[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.95 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel1.text(x_pos_custom, 0.72, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel1.text(x_pos_custom, 0.68, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + + + panel1.set_yticklabels(ylabels, fontsize=30) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.6,0.6,0.6], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + + if percentage: + plt.ylabel("Percentage of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='gray', width=2) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + + # =======================================OLD INDEL-TSB PLOT================================================================================== + # elif plot_type == '96' or plot_type == 'ID96' or plot_type == '96ID' or plot_type == 'IDSB': + # with open(matrix_path) as f: + # next(f) + # first_line = f.readline() + # first_line = first_line.strip().split("\t") + # mutation_type = first_line[0] + # mutation_type_list = mutation_type.split(":") + # if len(mutation_type_list) != 5: + # print(mutation_type_list) + # sys.exit("The matrix does not match the correct ID-96 format. Please check you formatting and rerun this plotting function.") + + # pp = PdfPages(output_path + 'ID_96_plots_' + project + '.pdf') + + # indel_types = ['1:Del:C:1', '1:Del:C:2', '1:Del:C:3', '1:Del:C:4', '1:Del:C:5', '1:Del:C:6' + # '1:Del:T:1', '1:Del:T:2', '1:Del:T:3', '1:Del:T:4', '1:Del:T:5', '1:Del:T:6' + # '1:Ins:C:0', '1:Ins:C:1', '1:Ins:C:2', '1:Ins:C:3', '1:Ins:C:4', '1:Ins:C:5', + # '1:Ins:T:0', '1:Ins:T:1', '1:Ins:T:2', '1:Ins:T:3', '1:Ins:T:4', '1:Ins:T:5'] + + # sig_probs = False + # mutations = OrderedDict() + # with open (matrix_path) as f: + # first_line = f.readline() + # samples = first_line.strip().split("\t") + # samples = samples[1:] + # for sample in samples: + # mutations[sample] = OrderedDict() + # mutations[sample]['1DelC'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + # mutations[sample]['1DelT'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + # mutations[sample]['1InsC'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + # mutations[sample]['1InsT'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + + # for lines in f: + # line = lines.strip().split() + # categories = line[0].split(":") + # if categories[1] != '1': + # break + # else: + # mut_type = categories[1] + categories[2] + categories[3] + # bias = categories[0] + # if bias != 'T' and bias != 'U': + # continue + # else: + # repeat_size = int(categories[4]) + # sample_index = 1 + # for sample in samples: + # if mut_type in mutations[sample]: + # if percentage: + # mutCount = float(line[sample_index]) + # if mutCount < 1 and mutCount > 0: + # sig_probs = True + # else: + # mutCount = int(line[sample_index]) + # if bias == 'T': + # mutations[sample][mut_type][repeat_size][0] = mutCount + # else: + # mutations[sample][mut_type][repeat_size][1] = mutCount + # else: + # continue + # sample_index += 1 + + # for sample in mutations: + # total_count = sum(sum(sum(tsb) for tsb in nuc) for nuc in mutations[sample].values()) + # plt.rcParams['axes.linewidth'] = 2 + # plot1 = plt.figure(figsize=(15,13)) + # plt.rc('axes', edgecolor='black') + # panel1 = plt.axes([0.12, 0.12, 0.8, 0.77]) + # xlabels = [] + + # x = 0.3 + # ymax = 0 + # colors = [[253/256,190/256,111/256], [255/256,128/256,2/256], [176/256,221/256,139/256], [54/256,161/256,46/256]] + + # i = 0 + # for key in mutations[sample]: + # l = 1 + # for seq in mutations[sample][key]: + # xlabels.append(l) + # if percentage: + # trans = plt.bar(x, seq[0]/total_count*100,width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + # x += 0.2 + # untrans = plt.bar(x, seq[1]/total_count*100,width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + # x += 0.8 + # if seq[0]/total_count*100 > ymax: + # ymax = seq[0]/total_count*100 + # if seq[1]/total_count*100 > ymax: + # ymax = seq[1]/total_count*100 + # else: + # trans = plt.bar(x, seq[0],width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + # x += 0.2 + # untrans = plt.bar(x, seq[1],width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + # x += 0.8 + # if seq[0] > ymax: + # ymax = seq[0] + # if seq[1] > ymax: + # ymax = seq[1] + # l += 1 + # i += 1 + + # x = .125 + # y_top = .8975 + # #y_bottom = .06525 + # y_bottom = .075 + # y = int(ymax*1.25) + # y2 = y+2 + + + + + + # for i in range(0, 4, 1): + # panel1.add_patch(plt.Rectangle((x,y_top), .185, .037, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + # panel1.add_patch(plt.Rectangle((x,y_bottom), .185, .037, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + # x += .202 + + + # yText = y_top + .005 + # plt.text(.205, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + # plt.text(.407, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + # plt.text(.609, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + # plt.text(.811, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + + # yText_labels_top = yText + .05 + # yText_labels_bottom = y_bottom - .03 + # yText_labels_bottom_sec = yText_labels_bottom -.025 + + # plt.text(.23, yText_labels_top, '1bp Deletion', fontsize=35, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + # plt.text(.634, yText_labels_top, '1bp Insertion', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + # plt.text(.18, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=30, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + # plt.text(.58, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=30, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + # x = .127 + # yText_labels_bottom = y_bottom - 0.025 + + # for l in range (0, 4, 1): + # if l < 2: + # for i in range(1, 6, 1): + # plt.text(x, yText_labels_bottom, str(i), fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + # x += 0.034 + # x -= 0.008 + # plt.text(x, yText_labels_bottom, '6+', fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + # x += 0.041 + # else: + # for i in range(0, 5, 1): + # plt.text(x, yText_labels_bottom, str(i), fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + # x += 0.033 + # x -= 0.005 + # plt.text(x, yText_labels_bottom, '5+', fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + # x += 0.044 + + # if y <= 4: + # y += 4 + + # while y%4 != 0: + # y += 1 + # ytick_offest = int(y/4) + + + # x_shaded = 0 + # for i in range(0, 4, 1): + # panel1.add_patch(plt.Rectangle((x_shaded,0), 6, y, facecolor=colors[i], zorder=0, alpha = 0.25, edgecolor='grey')) + # x_shaded += 6 + + # if percentage: + # ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + # ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + # str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + # else: + # ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + # ylabels= [0, ytick_offest, ytick_offest*2, + # ytick_offest*3, ytick_offest*4] + + + # if not percentage: + # ylabels = ['{:,}'.format(int(x)) for x in ylabels] + # if len(ylabels[-1]) > 3: + # ylabels_temp = [] + # if len(ylabels[-1]) > 7: + # for label in ylabels: + # if len(label) > 7: + # ylabels_temp.append(label[0:-8] + "m") + # elif len(label) > 3: + # ylabels_temp.append(label[0:-4] + "k") + # else: + # ylabels_temp.append(label) + + # else: + # for label in ylabels: + # if len(label) > 3: + # ylabels_temp.append(label[0:-4] + "k") + # else: + # ylabels_temp.append(label) + # ylabels = ylabels_temp + + # panel1.set_xlim([0, 23.8]) + # panel1.set_ylim([0, y]) + # panel1.set_yticks(ylabs) + + # if sig_probs: + # plt.text(0.13, 0.85, sample, fontsize=33, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + # else: + # plt.text(0.13, 0.85, sample + ": " + "{:,}".format(int(total_count)) + " transcribed indels", fontsize=33, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + # panel1.set_yticklabels(ylabels, fontsize=30) + # plt.gca().yaxis.grid(True) + # plt.gca().grid(which='major', axis='y', color=[0.6,0.6,0.6], zorder=1) + # panel1.set_xlabel('') + # panel1.set_ylabel('') + # plt.legend(handles=[trans, untrans], prop={'size':20}) + + # if percentage: + # plt.ylabel("Percentage of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + # else: + # plt.ylabel("Number of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + + # panel1.tick_params(axis='both',which='both',\ + # bottom=False, labelbottom=False,\ + # left=False, labelleft=True,\ + # right=False, labelright=False,\ + # top=False, labeltop=False,\ + # direction='in', length=25, colors='gray', width=2) + + # [i.set_color("black") for i in plt.gca().get_yticklabels()] + + + + + + # pp.savefig(plot1) + # plt.close() + # pp.close() + # =================================================================================================================================== + + + + elif plot_type == 'INDEL_simple' or plot_type == 'simple_INDEL' or plot_type == 'ID_simple' or plot_type == 'simple_ID' or plot_type == '28': + with open(matrix_path) as f: + next(f) + first_line = f.readline() + first_line = first_line.strip().split() + mutation_type = first_line[0] + mutation_type_list = mutation_type.split(":") + if len(mutation_type_list) != 4: + sys.exit("The matrix does not match the correct SBS96 format. Please check you formatting and rerun this plotting function.") + pp = PdfPages(output_path + 'ID_simple_plots_' + project + '.pdf') + + indel_types = ['1:Del:C:1', '1:Del:C:2', '1:Del:C:3', '1:Del:C:4', '1:Del:C:5', '1:Del:C:6' + '1:Del:T:1', '1:Del:T:2', '1:Del:T:3', '1:Del:T:4', '1:Del:T:5', '1:Del:T:6' + '1:Ins:C:0', '1:Ins:C:1', '1:Ins:C:2', '1:Ins:C:3', '1:Ins:C:4', '1:Ins:C:5', + '1:Ins:T:0', '1:Ins:T:1', '1:Ins:T:2', '1:Ins:T:3', '1:Ins:T:4', '1:Ins:T:5', + 'long_Del', 'long_Ins', 'MH', 'complex'] + + mutations = OrderedDict() + + try: + with open (matrix_path) as f: + first_line = f.readline() + samples = first_line.strip().split("\t") + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['1DelC'] = [0,0,0,0,0,0] + mutations[sample]['1DelT'] = [0,0,0,0,0,0] + mutations[sample]['1InsC'] = [0,0,0,0,0,0] + mutations[sample]['1InsT'] = [0,0,0,0,0,0] + mutations[sample]['long_Del'] = [0] + mutations[sample]['long_Ins'] = [0] + mutations[sample]['MH'] = [0] + mutations[sample]['complex'] = [0] + + for lines in f: + line = lines.strip().split() + categories = line[0].split(":") + if len(categories) < 2: + mut_type = categories[0] + repeat_size = 0 + else: + mut_type = categories[0] + categories[1] + categories[2] + repeat_size = int(categories[3]) + sample_index = 1 + + for sample in samples: + #if mut_type in mutations[sample].keys(): + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + mutations[sample][mut_type][repeat_size] = mutCount + + # else: + # if percentage: + # mutCount = float(line[sample_index]) + # else: + # mutCount = int(line[sample_index]) + # if int(mut_type[0]) > 1: + # repeat_size = 0 + # if categories[2] == 'M': + # mut_type = 'MH' + # mutations[sample][mut_type][repeat_size] += mutCount + # else: + # if categories[1] == 'Del': + # mut_type = 'Del' + # mutations[sample][mut_type][repeat_size] += mutCount + # else: + # mut_type = 'Ins' + # mutations[sample][mut_type][repeat_size] += mutCount + + #continue + sample_index += 1 + + for sample in mutations: + total_count = sum(sum(nuc) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(15,13)) + plt.rc('axes', edgecolor='black') + panel1 = plt.axes([0.12, 0.12, 0.8, 0.77]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[253/256,190/256,111/256], [255/256,128/256,2/256], [176/256,221/256,139/256], [54/256,161/256,46/256], + #[188/256,25/256,26/256], + [23/256,100/256,171/256],[98/256,64/256,155/256], [98/256,64/256,155/256]] + + i = 0 + for key in mutations[sample]: + l = 1 + for seq in mutations[sample][key]: + xlabels.append(l) + if percentage: + if total_count > 0: + plt.bar(x, seq/total_count*100,width=0.4,color=colors[i],align='center', zorder=1000) + if seq/total_count*100 > ymax: + ymax = seq/total_count*100 + else: + plt.bar(x, seq,width=0.4,color=colors[i],align='center', zorder=1000) + if seq > ymax: + ymax = seq + x += 1 + l += 1 + if i < 4: + i += 1 + x = .126 + y_top = .9 + y_bottom = .075 + y = int(ymax*1.25) + y2 = y+2 + + for i in range(0, 4, 1): + panel1.add_patch(plt.Rectangle((x,y_top), .154, .037, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .154, .037, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .1715 + + x -= .001 + panel1.add_patch(plt.Rectangle((x,y_top), .098, .037, facecolor=colors[i+1], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .098, .037, facecolor=colors[i+1], clip_on=False, transform=plt.gcf().transFigure)) + + yText = y_top + .0055 + plt.text(.185, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.36, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + plt.text(.53, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.705, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + + yText_labels_top = yText + .045 + yText_labels_bottom = y_bottom - .03 + yText_labels_bottom_sec = yText_labels_bottom -.025 + + plt.text(.2, yText_labels_top, '1bp Deletion', fontsize=35, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.54, yText_labels_top, '1bp Insertion', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.155, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=30, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.505, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=30, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.827, yText_labels_top, '>1bp', fontsize=30, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.83, yText_labels_bottom_sec, 'Type', fontsize=30, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + x = .127 + yText_labels_bottom = y_bottom - 0.025 + + for l in range (0, 4, 1): + if l < 2: + for i in range(1, 6, 1): + plt.text(x, yText_labels_bottom, str(i), fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += 0.028 + x -= 0.005 + plt.text(x, yText_labels_bottom, '6+', fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += 0.037 + else: + if l == 2: + x += 0 + for i in range(0, 5, 1): + plt.text(x, yText_labels_bottom, str(i), fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += 0.028 + x -= 0.005 + plt.text(x, yText_labels_bottom, '5+', fontsize=25, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += 0.037 + + yText_labels_bottom += 0.01 + plt.text(x, yText_labels_bottom, 'Del', fontsize=17, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure, rotation='vertical') + x += 0.026 + plt.text(x, yText_labels_bottom, 'Ins', fontsize=17, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure, rotation='vertical') + x += 0.0295 + yText_labels_bottom += 0.003 + plt.text(x, yText_labels_bottom, 'MH', fontsize=17, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure, rotation='vertical') + x += 0.0295 + yText_labels_bottom += 0.005 + plt.text(x, yText_labels_bottom, 'COMP', fontsize=10, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure, rotation='vertical') + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + + + + panel1.set_xlim([0, 28]) + panel1.set_ylim([0, y]) + panel1.set_yticks(ylabs) + + if sig_probs: + plt.text(0.13, 0.85, sample, fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.13, 0.85, sample + ": " + "{:,}".format(int(total_count)) + " indels", fontsize=40, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + panel1.set_yticklabels(ylabels, fontsize=30) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.6,0.6,0.6], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + + if percentage: + plt.ylabel("Percentage of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='gray', width=2) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + + + pp.savefig(plot1) + plt.close() + pp.close() + + except: + print("There may be an issue with the formatting of you matrix file.") + os.remove(output_path + 'ID_simple_plots_' + project + '.pdf') + + elif plot_type == '96' or plot_type == 'ID96' or plot_type == '96ID' or plot_type == 'IDSB' or plot_type == '415': + with open(matrix_path) as f: + next(f) + first_line = f.readline() + first_line = first_line.strip().split("\t") + mutation_type = first_line[0] + mutation_type_list = mutation_type.split(":") + if len(mutation_type_list) != 5: + print(mutation_type_list) + sys.exit("The matrix does not match the correct ID-96 format. Please check you formatting and rerun this plotting function.") + + pp = PdfPages(output_path + 'ID_TSB_plots_' + project + '.pdf') + + indel_types_tsb = [] + tsb_I = ['T','U','N','B','Q'] + indel_types = ['1:Del:C:0', '1:Del:C:1', '1:Del:C:2', '1:Del:C:3', '1:Del:C:4', '1:Del:C:5', + '1:Del:T:0', '1:Del:T:1', '1:Del:T:2', '1:Del:T:3', '1:Del:T:4', '1:Del:T:5', + '1:Ins:C:0', '1:Ins:C:1', '1:Ins:C:2', '1:Ins:C:3', '1:Ins:C:4', '1:Ins:C:5', + '1:Ins:T:0', '1:Ins:T:1', '1:Ins:T:2', '1:Ins:T:3', '1:Ins:T:4', '1:Ins:T:5', + # >1bp INDELS + '2:Del:R:0', '2:Del:R:1', '2:Del:R:2', '2:Del:R:3', '2:Del:R:4', '2:Del:R:5', + '3:Del:R:0', '3:Del:R:1', '3:Del:R:2', '3:Del:R:3', '3:Del:R:4', '3:Del:R:5', + '4:Del:R:0', '4:Del:R:1', '4:Del:R:2', '4:Del:R:3', '4:Del:R:4', '4:Del:R:5', + '5:Del:R:0', '5:Del:R:1', '5:Del:R:2', '5:Del:R:3', '5:Del:R:4', '5:Del:R:5', + '2:Ins:R:0', '2:Ins:R:1', '2:Ins:R:2', '2:Ins:R:3', '2:Ins:R:4', '2:Ins:R:5', + '3:Ins:R:0', '3:Ins:R:1', '3:Ins:R:2', '3:Ins:R:3', '3:Ins:R:4', '3:Ins:R:5', + '4:Ins:R:0', '4:Ins:R:1', '4:Ins:R:2', '4:Ins:R:3', '4:Ins:R:4', '4:Ins:R:5', + '5:Ins:R:0', '5:Ins:R:1', '5:Ins:R:2', '5:Ins:R:3', '5:Ins:R:4', '5:Ins:R:5', + #MicroHomology INDELS + '2:Del:M:1', '3:Del:M:1', '3:Del:M:2', '4:Del:M:1', '4:Del:M:2', '4:Del:M:3', + '5:Del:M:1', '5:Del:M:2', '5:Del:M:3', '5:Del:M:4', '5:Del:M:5'] + + for indels in indel_types: + for tsbs in tsb_I: + indel_types_tsb.append(tsbs + ":" + indels) + + sig_probs = False + mutations = OrderedDict() + try: + with open (matrix_path) as f: + first_line = f.readline() + if pcawg: + samples = first_line.strip().split(",") + samples = samples[4:] + samples = [x.replace('"','') for x in samples] + else: + samples = first_line.strip().split("\t") + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['1DelC'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['1DelT'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['1InsC'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['1InsT'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['2DelR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['3DelR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['4DelR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['5DelR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['2InsR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['3InsR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['3InsR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['4InsR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['5InsR'] = [[0,0],[0,0],[0,0],[0,0],[0,0],[0,0]] + mutations[sample]['2DelM'] = [[0,0]] + mutations[sample]['3DelM'] = [[0,0],[0,0]] + mutations[sample]['4DelM'] = [[0,0],[0,0],[0,0]] + mutations[sample]['5DelM'] = [[0,0],[0,0],[0,0],[0,0],[0,0]] + + for lines in f: + if pcawg: + line = lines.strip().split(",") + line = [x.replace('"','') for x in line] + if line[1] == 'repeats': + mut_type = line[2][0] + line[0][0] + line[0][1].lower() + line[0][2].lower() + "R" + else: + mut_type = line[2][0] + line[0][0] + line[0][1].lower() + line[0][2].lower() + line[1][0] + try: + repeat_size = int(line[3]) + except: + repeat_size = int(line[3][0]) + if line[1] == 'MH': + repeat_size -= 1 + sample_index = 4 + else: + line = lines.strip().split() + if line[0] not in indel_types_tsb: + continue + categories = line[0].split(":") + bias = categories[0] + if bias == 'B' or bias == 'N' or bias == 'Q': + continue + mut_type = categories[1] + categories[2] + categories[3] + + repeat_size = int(categories[4]) + if categories[3] == 'M': + repeat_size -= 1 + sample_index = 1 + + for sample in samples: + if mut_type in mutations[sample].keys(): + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + if bias == 'T': + mutations[sample][mut_type][repeat_size][0] = mutCount + else: + mutations[sample][mut_type][repeat_size][1] = mutCount + else: + continue + sample_index += 1 + + sample_count = 0 + for sample in mutations.keys(): + total_count = sum(sum(sum(tsb) for tsb in nuc) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(43.93,12)) + plt.rc('axes', edgecolor='black') + panel1 = plt.axes([0.045, 0.17, 0.92, 0.65]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[253/256,190/256,111/256], [255/256,128/256,2/256], [176/256,221/256,139/256], [54/256,161/256,46/256], + [253/256,202/256,181/256], [252/256,138/256,106/256], [241/256,68/256,50/256], [188/256,25/256,26/256], + [208/256,225/256,242/256], [148/256,196/256,223/256], [74/256,152/256,201/256], [23/256,100/256,171/256], + [226/256,226/256,239/256], [182/256,182/256,216/256], [134/256,131/256,189/256], [98/256,64/256,155/256]] + + i = 0 + for key in mutations[sample]: + l = 1 + for seq in mutations[sample][key]: + xlabels.append(l) + if percentage: + if total_count > 0: + trans = plt.bar(x, seq[0]/total_count*100,width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.2 + untrans = plt.bar(x, seq[1]/total_count*100,width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + if seq[0]/total_count*100 > ymax: + ymax = seq[0]/total_count*100 + if seq[1]/total_count*100 > ymax: + ymax = seq[1]/total_count*100 + + else: + trans = plt.bar(x, seq[0],width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.2 + untrans = plt.bar(x, seq[1],width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + if seq[0] > ymax: + ymax = seq[0] + if seq[1] > ymax: + ymax = seq[1] + + x += 0.799 + l += 1 + i += 1 + + x = .0475 + y_top = .827 + y_bottom = .114 + y = int(ymax*1.25) + y2 = y+2 + for i in range(0, 12, 1): + panel1.add_patch(plt.Rectangle((x,y_top), .0595, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .0595, .05, facecolor=colors[i], clip_on=False, transform=plt.gcf().transFigure)) + x += .0665 + + panel1.add_patch(plt.Rectangle((x-.001,y_top), .006, .05, facecolor=colors[12], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x-.001,y_bottom), .006, .05, facecolor=colors[12], clip_on=False, transform=plt.gcf().transFigure)) + x +=.011 + panel1.add_patch(plt.Rectangle((x,y_top), .0155, .05, facecolor=colors[13], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .0155, .05, facecolor=colors[13], clip_on=False, transform=plt.gcf().transFigure)) + x += .022 + panel1.add_patch(plt.Rectangle((x,y_top), .027, .05, facecolor=colors[14], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .027, .05, facecolor=colors[14], clip_on=False, transform=plt.gcf().transFigure)) + x += .0335 + panel1.add_patch(plt.Rectangle((x,y_top), .049, .05, facecolor=colors[15], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((x,y_bottom), .049, .05, facecolor=colors[15], clip_on=False, transform=plt.gcf().transFigure)) + + + + + yText = y_top + .01 + plt.text(.072, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.1385, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + plt.text(.205, yText, 'C', fontsize=40, fontname='Times New Roman', fontweight='bold', transform=plt.gcf().transFigure) + plt.text(.2715, yText, 'T', fontsize=40, fontname='Times New Roman', fontweight='bold', color='white', transform=plt.gcf().transFigure) + plt.text(.338, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.4045, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.471, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.5375, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + plt.text(.604, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.6705, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.737, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.8035, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + plt.text(.844, yText, '2', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.861, yText, '3', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.888, yText, '4', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.93, yText, '5+', fontsize=40, fontweight='bold', fontname='Times New Roman', color='white', transform=plt.gcf().transFigure) + + yText_labels_top = yText + .075 + yText_labels_bottom = y_bottom - .03 + yText_labels_bottom_sec = yText_labels_bottom - .045 + + plt.text(.08, yText_labels_top, '1bp Deletion', fontsize=40, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.21, yText_labels_top, '1bp Insertion', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.375, yText_labels_top, '>1bp Deletion at Repeats\n (Deletion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.64, yText_labels_top, '>1bp Insertions at Repeats\n (Insertion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.85, yText_labels_top, ' Mircohomology\n(Deletion Length)', fontsize=40, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + plt.text(.058, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=35, fontname='Times New Roman', weight='bold', color='black', transform=plt.gcf().transFigure) + plt.text(.19, yText_labels_bottom_sec, 'Homopolymer Length', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.39, yText_labels_bottom_sec, 'Number of Repeat Units', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.65, yText_labels_bottom_sec, 'Number of Repeat Units', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + plt.text(.85, yText_labels_bottom_sec, 'Mircohomology Length', fontsize=35, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + x = .0477 + for i in range (0, 8, 1): + if i != 2 and i != 3: + plt.text(x, yText_labels_bottom, '1 2 3 4 5 6+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + else: + plt.text(x, yText_labels_bottom, '0 1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + x += .0665 + + for i in range (0, 4, 1): + plt.text(x, yText_labels_bottom, '0 1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .0665 + + plt.text(x, yText_labels_bottom, '1', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .011 + plt.text(x, yText_labels_bottom, '1 2', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .022 + plt.text(x, yText_labels_bottom, '1 2 3', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + x += .0335 + plt.text(x, yText_labels_bottom, '1 2 3 4 5+', fontsize=32, fontweight='bold', fontname='Times New Roman', color='black', transform=plt.gcf().transFigure) + + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + labs = np.arange(0.375,83.375,1) + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + panel1.set_xlim([0, 83]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + + if sig_probs: + plt.text(0.0475, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.0475, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " indels", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_middle: + if len(custom_text_middle[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.95 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel1.text(x_pos_custom, 0.72, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel1.text(x_pos_custom, 0.68, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + + + panel1.set_yticklabels(ylabels, fontsize=30) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.6,0.6,0.6], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + panel1.legend(handles=[trans, untrans], prop={'size':30}) + + + if percentage: + plt.ylabel("Percentage of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Indels", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=False,\ + left=False, labelleft=True,\ + right=False, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='gray', width=2) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + + pp.savefig(plot1) + plt.close() + sample_count += 1 + pp.close() + + except: + print("There may be an issue with the formatting of you matrix file.") + os.remove(output_path + 'ID_TSB_plots_' + project + '.pdf') + + + + else: + print("The provided plot_type: ", plot_type, " is not supported by this plotting function") + +def plotDBS(matrix_path, output_path, project, plot_type, percentage=False, custom_text_upper=None, custom_text_middle=None, custom_text_bottom=None): + + # if 'roman' in matplotlib.font_manager.weight_dict: + # del matplotlib.font_manager.weight_dict['roman'] + # matplotlib.font_manager._rebuild() + plot_custom_text = False + pcawg = False + sig_probs = False + buff_list = dict() + + if plot_type == '78' or plot_type == '78DBS' or plot_type == 'DBS78': + + first_line=matrix_path.iloc[0,:] + mutation_type = first_line[0] + if first_line[0][2] != ">": + pcawg = True + if len(mutation_type) != 5 and first_line[0][2] == ">": + sys.exit("The matrix does not match the correct DBS96 format. Please check you formatting and rerun this plotting function.") + + dinucs = ['TT>GG','TT>CG','TT>AG','TT>GC','TT>CC','TT>AC','TT>GA','TT>CA','TT>AA','AC>CA','AC>CG','AC>CT','AC>GA', + 'AC>GG','AC>GT','AC>TA','AC>TG','AC>TT','CT>AA','CT>AC','CT>AG','CT>GA','CT>GC','CT>GG','CT>TG','CT>TC', + 'CT>TA','AT>CA','AT>CC','AT>CG','AT>GA','AT>GC','AT>TA','TG>GT','TG>CT','TG>AT','TG>GC','TG>CC','TG>AC', + 'TG>GA','TG>CA','TG>AA','CC>AA','CC>AG','CC>AT','CC>GA','CC>GG','CC>GT','CC>TA','CC>TG','CC>TT','CG>AT', + 'CG>GC','CG>GT','CG>TC','CG>TA','CG>TT','TC>GT','TC>CT','TC>AT','TC>GG','TC>CG','TC>AG','TC>GA','TC>CA', + 'TC>AA','GC>AA','GC>AG','GC>AT','GC>CA','GC>CG','GC>TA','TA>GT','TA>CT','TA>AT','TA>GG','TA>CG','TA>GC'] + + revcompl = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A'}[B] for B in x][::-1]) + mutations = OrderedDict() + + first_line=matrix_path.iloc[0,:] + if pcawg: + samples = matrix_path.columns[:] + samples = samples[2:] + samples = [x.replace('"','') for x in samples] + else: + samples = matrix_path.columns[:] + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['AC'] = OrderedDict() + mutations[sample]['AT'] = OrderedDict() + mutations[sample]['CC'] = OrderedDict() + mutations[sample]['CG'] = OrderedDict() + mutations[sample]['CT'] = OrderedDict() + mutations[sample]['GC'] = OrderedDict() + mutations[sample]['TA'] = OrderedDict() + mutations[sample]['TC'] = OrderedDict() + mutations[sample]['TG'] = OrderedDict() + mutations[sample]['TT'] = OrderedDict() + + + for lines_tmp in range(0,matrix_path.shape[0]): + if pcawg: + line = matrix_path.iloc[lines_tmp,:] + line = [x.replace('"','') for x in line] + mut = line[0] + ">" + line[1] + nuc = line[1] + mut_type = line[0] + if mut not in dinucs: + nuc = revcompl(nuc) + mut_type = revcompl(mut_type) + sample_index = 2 + else: + line = matrix_path.iloc[lines_tmp,:] + mut = line[0] + nuc = line[0][3:] + mut_type = line[0][0:2] + if mut not in dinucs: + nuc = revcompl(nuc) + mut_type = revcompl(mut_type) + sample_index = 1 + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + mutations[sample][mut_type][nuc] = mutCount + sample_index += 1 + + sample_count = 0 + for sample in mutations.keys(): + total_count = sum(sum(nuc.values()) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 4 + plot1 = plt.figure(figsize=(43.93,9.92)) + plt.rc('axes', edgecolor='grey') + panel1 = plt.axes([0.04, 0.09, 0.95, 0.77]) + xlabels = [] + + x = 0.4 + ymax = 0 + colors = [[3/256,189/256,239/256], [3/256,102/256,204/256],[162/256,207/256,99/256], + [1/256,102/256,1/256], [255/256,153/256,153/256], [228/256,41/256,38/256], + [255/256,178/256,102/256], [255/256,128/256,1/256], [204/256,153/256,255/256], + [76/256,1/256,153/256]] + i = 0 + for key in mutations[sample]: + muts = mutations[sample][key].keys() + muts = sorted(muts) + for seq in muts: + xlabels.append(seq) + if percentage: + if total_count > 0: + plt.bar(x, mutations[sample][key][seq]/total_count*100,width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq]/total_count*100 > ymax: + ymax = mutations[sample][key][seq]/total_count*100 + else: + plt.bar(x, mutations[sample][key][seq],width=0.4,color=colors[i],align='center', zorder=1000) + if mutations[sample][key][seq] > ymax: + ymax = mutations[sample][key][seq] + x += 1 + i += 1 + + x = .043 + y3 = .87 + y = ymax*1.25 + y2 = y+2 + i = 0 + panel1.add_patch(plt.Rectangle((.043,y3), .101, .05, facecolor=colors[0], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.151,y3), .067, .05, facecolor=colors[1], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.225,y3), .102, .05, facecolor=colors[2], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.334,y3), .067, .05, facecolor=colors[3], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.408,y3), .102, .05, facecolor=colors[4], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.517,y3), .067, .05, facecolor=colors[5], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.591,y3), .067, .05, facecolor=colors[6], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.665,y3), .102, .05, facecolor=colors[7], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.774,y3), .102, .05, facecolor=colors[8], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.883,y3), .102, .05, facecolor=colors[9], clip_on=False, transform=plt.gcf().transFigure)) + + yText = y3 + .06 + plt.text(.07, yText, 'AC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.163, yText, 'AT>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.255, yText, 'CC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.345, yText, 'CG>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.435, yText, 'CT>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.527, yText, 'GC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.6, yText, 'TA>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.69, yText, 'TC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.8, yText, 'TG>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.915, yText, 'TT>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if y <= 4: + y += 4 + + if percentage: + ytick_offest = round((y/4), 1) + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + # if y < 10: + # if y/4 - int(y/4) > 0.5: + # ytick_offest = int(y/4) + 1 + # else: + # ytick_offest = int(y/4) + if y < 4: + y = 4 + #else: + ytick_offest = int(y/4) + if ytick_offest == 0: + ytick_offest = 1 + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + if y < 4: + y = 4 + + if sig_probs: + plt.text(0.045, 0.75, sample, fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.045, 0.75, sample + ": " + "{:,}".format(int(total_count)) + " double subs", fontsize=60, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + custom_text_upper_plot = '' + try: + custom_text_upper[sample_count] + except: + custom_text_upper = False + try: + custom_text_middle[sample_count] + except: + custom_text_middle = False + try: + custom_text_bottom[sample_count] + except: + custom_text_bottom = False + + if custom_text_upper: + plot_custom_text = True + if len(custom_text_upper[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + if custom_text_bottom: + if len(custom_text_bottom[sample_count]) > 40: + print("To add a custom text, please limit the string to <40 characters including spaces.") + plot_custom_text = False + + if plot_custom_text: + x_pos_custom = 0.98 + if custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + "\n" + custom_text_middle[sample_count] + if custom_text_bottom: + custom_text_upper_plot += "\n" + custom_text_bottom[sample_count] + + if custom_text_upper and not custom_text_middle: + custom_text_upper_plot = custom_text_upper[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif custom_text_upper and custom_text_middle: + if not custom_text_bottom: + panel1.text(x_pos_custom, 0.75, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + else: + panel1.text(x_pos_custom, 0.7, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + elif not custom_text_upper and custom_text_middle: + custom_text_upper_plot = custom_text_middle[sample_count] + panel1.text(x_pos_custom, 0.78, custom_text_upper_plot, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure, ha='right') + + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + + labs = np.arange(0.44,78.44,1) + panel1.set_xlim([0, 78]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + panel1.set_xticklabels(xlabels, rotation='vertical', fontsize=30, color='grey', fontname='Courier New', verticalalignment='top', fontweight='bold') + + panel1.set_yticklabels(ylabels, fontsize=25) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.93,0.93,0.93], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + + if percentage: + plt.ylabel("Percentage of Double Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Double Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=True,\ + left=True, labelleft=True,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='lightgray', width=2) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + [i.set_color("grey") for i in plt.gca().get_xticklabels()] + + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + sample_count += 1 + return buff_list + #pp.close() + # except: + # print("There may be an issue with the formatting of you matrix file.") + # os.remove(output_path + 'DBS_78_plots_' + project + '.pdf') + + elif plot_type == '312' or plot_type == '78SB' or plot_type == 'SB78' or plot_type == '186': + with open(matrix_path) as f: + next(f) + first_line = f.readline() + first_line = first_line.strip().split() + mutation_type = first_line[0] + if len(mutation_type) != 7 and mutation_type[1] != ':': + sys.exit("The matrix does not match the correct SBS96 format. Please check you formatting and rerun this plotting function.") + + #pp = PdfPages(output_path + 'DBS_186_plots_' + project + '.pdf') + + dinucs = ['TT>GG','TT>CG','TT>AG','TT>GC','TT>CC','TT>AC','TT>GA','TT>CA','TT>AA', + 'CT>AA','CT>AC','CT>AG','CT>GA','CT>GC','CT>GG','CT>TG','CT>TC','CT>TA', + 'CC>AA','CC>AG','CC>AT','CC>GA','CC>GG','CC>GT','CC>TA','CC>TG','CC>TT', + 'TC>GT','TC>CT','TC>AT','TC>GG','TC>CG','TC>AG','TC>GA','TC>CA','TC>AA'] + + revcompl = lambda x: ''.join([{'A':'T','C':'G','G':'C','T':'A','>':'>'}[B] for B in x][::-1]) + mutations = OrderedDict() + + with open (matrix_path) as f: + first_line = f.readline() + samples = first_line.strip().split("\t") + samples = samples[1:] + for sample in samples: + mutations[sample] = OrderedDict() + mutations[sample]['CC'] = OrderedDict() + mutations[sample]['CT'] = OrderedDict() + mutations[sample]['TC'] = OrderedDict() + mutations[sample]['TT'] = OrderedDict() + + for lines in f: + line = lines.strip().split() + mut = line[0][2:] + nuc = line[0][5:] + mut_type = line[0][2:4] + bias = line[0][0] + if bias == 'N' or bias == 'B' or bias == 'Q': + continue + else: + if mut not in dinucs: + if revcompl(mut) not in dinucs: + continue + nuc = revcompl(nuc) + mut_type = revcompl(mut_type) + sample_index = 1 + + for sample in samples: + if percentage: + mutCount = float(line[sample_index]) + if mutCount < 1 and mutCount > 0: + sig_probs = True + else: + mutCount = int(line[sample_index]) + if nuc not in mutations[sample][mut_type]: + mutations[sample][mut_type][nuc] = [0,0] + if bias == 'T': + mutations[sample][mut_type][nuc][0] = mutCount + else: + mutations[sample][mut_type][nuc][1] = mutCount + sample_index += 1 + + for sample in mutations.keys(): + total_count = sum(sum(sum(tsb) for tsb in nuc.values()) for nuc in mutations[sample].values()) + plt.rcParams['axes.linewidth'] = 2 + plot1 = plt.figure(figsize=(21,9.92)) + plt.rc('axes', edgecolor='lightgray') + panel1 = plt.axes([0.07, 0.09, 0.92, 0.77]) + xlabels = [] + + x = 0.3 + ymax = 0 + i = 0 + colors = [[3/256,189/256,239/256], [3/256,102/256,204/256],[162/256,207/256,99/256], + [1/256,102/256,1/256], [255/256,153/256,153/256], [228/256,41/256,38/256], + [255/256,178/256,102/256], [255/256,128/256,1/256], [204/256,153/256,255/256], + [76/256,1/256,153/256]] + for key in mutations[sample]: + muts = mutations[sample][key].keys() + muts = sorted(muts) + for seq in muts: + xlabels.append(seq) + if percentage: + try: + trans = plt.bar(x, mutations[sample][key][seq][0]/total_count*100,width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.2 + untrans = plt.bar(x, mutations[sample][key][seq][1]/total_count*100,width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + x += .8 + if mutations[sample][key][seq][0]/total_count*100 > ymax: + ymax = mutations[sample][key][seq][0]/total_count*100 + if mutations[sample][key][seq][1]/total_count*100 > ymax: + ymax = mutations[sample][key][seq][1]/total_count*100 + except: + trans = plt.bar(x, 0,width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + untrans = plt.bar(x, 0, width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + + else: + trans = plt.bar(x, mutations[sample][key][seq][0],width=0.2,color=[1/256,70/256,102/256],align='center', zorder=1000, label='Transcribed Strand') + x += 0.2 + untrans = plt.bar(x, mutations[sample][key][seq][1],width=0.2,color=[228/256,41/256,38/256],align='center', zorder=1000, label='Untranscribed Strand') + x += .8 + if mutations[sample][key][seq][0] > ymax: + ymax = mutations[sample][key][seq][0] + if mutations[sample][key][seq][1] > ymax: + ymax = mutations[sample][key][seq][1] + i += 1 + + + y3 = .87 + y = int(ymax*1.25) + + panel1.add_patch(plt.Rectangle((.075,y3), .218, .05, facecolor=colors[0], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.302,y3), .218, .05, facecolor=colors[2], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.532,y3), .218, .05, facecolor=colors[4], clip_on=False, transform=plt.gcf().transFigure)) + panel1.add_patch(plt.Rectangle((.765,y3), .218, .05, facecolor=colors[7], clip_on=False, transform=plt.gcf().transFigure)) + + yText = y3 + .06 + plt.text(.13, yText, 'CC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.37, yText, 'CT>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.59, yText, 'TC>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + plt.text(.83, yText, 'TT>NN', fontsize=40, fontweight='bold', fontname='Arial', transform=plt.gcf().transFigure) + + if y <= 4: + y += 4 + + while y%4 != 0: + y += 1 + ytick_offest = int(y/4) + + x_shaded = 0 + panel1.add_patch(plt.Rectangle((x_shaded,0), 8.9, y, facecolor=colors[0], zorder=0, alpha = 0.25, edgecolor='grey')) + x_shaded += 8.9 + panel1.add_patch(plt.Rectangle((x_shaded,0), 9, y, facecolor=colors[2], zorder=0, alpha = 0.25, edgecolor='grey')) + x_shaded += 9 + panel1.add_patch(plt.Rectangle((x_shaded,0), 9, y, facecolor=colors[4], zorder=0, alpha = 0.25, edgecolor='grey')) + x_shaded += 9 + panel1.add_patch(plt.Rectangle((x_shaded,0), 9.1, y, facecolor=colors[7], zorder=0, alpha = 0.25, edgecolor='grey')) + + + if percentage: + ylabs = [0, round(ytick_offest, 1), round(ytick_offest*2, 1), round(ytick_offest*3, 1), round(ytick_offest*4, 1)] + ylabels= [str(0), str(round(ytick_offest, 1)) + "%", str(round(ytick_offest*2, 1)) + "%", + str(round(ytick_offest*3, 1)) + "%", str(round(ytick_offest*4, 1)) + "%"] + else: + + if ytick_offest == 0: + ytick_offest = 1 + ylabs = [0, ytick_offest, ytick_offest*2, ytick_offest*3, ytick_offest*4] + ylabels= [0, ytick_offest, ytick_offest*2, + ytick_offest*3, ytick_offest*4] + + + if sig_probs: + plt.text(0.08, 0.8, sample, fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + else: + plt.text(0.08, 0.8, sample + ": " + "{:,}".format(int(total_count)) + " transcribed double subs", fontsize=35, weight='bold', color='black', fontname= "Arial", transform=plt.gcf().transFigure) + + if not percentage: + ylabels = ['{:,}'.format(int(x)) for x in ylabels] + if len(ylabels[-1]) > 3: + ylabels_temp = [] + if len(ylabels[-1]) > 7: + for label in ylabels: + if len(label) > 7: + ylabels_temp.append(label[0:-8] + "m") + elif len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + + else: + for label in ylabels: + if len(label) > 3: + ylabels_temp.append(label[0:-4] + "k") + else: + ylabels_temp.append(label) + ylabels = ylabels_temp + + + labs = np.arange(0.55,36.44,1) + panel1.set_xlim([0, 36]) + panel1.set_ylim([0, y]) + panel1.set_xticks(labs) + panel1.set_yticks(ylabs) + panel1.set_xticklabels(xlabels, rotation='vertical', fontsize=30, color='grey', fontname='Courier New', verticalalignment='top', fontweight='bold') + + panel1.set_yticklabels(ylabels, fontsize=25) + plt.gca().yaxis.grid(True) + plt.gca().grid(which='major', axis='y', color=[0.93,0.93,0.93], zorder=1) + panel1.set_xlabel('') + panel1.set_ylabel('') + panel1.legend(handles=[trans, untrans], prop={'size':30}) + + if percentage: + plt.ylabel("Percentage of Double Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + else: + plt.ylabel("Number of Double Base Substitutions", fontsize=35, fontname="Times New Roman", weight = 'bold') + + panel1.tick_params(axis='both',which='both',\ + bottom=False, labelbottom=True,\ + left=True, labelleft=True,\ + right=True, labelright=False,\ + top=False, labeltop=False,\ + direction='in', length=25, colors='lightgray', width=2) + + [i.set_color("black") for i in plt.gca().get_yticklabels()] + [i.set_color("grey") for i in plt.gca().get_xticklabels()] + + panel1.set_xlim([0, 36]) + buffer = io.BytesIO() + plt.savefig(buffer, format="png") + buff_list[sample]=buffer + plt.close() + return buff_list + #pp.close() + # except: + # print("There may be an issue with the formatting of you matrix file.") + # os.remove(output_path + 'DBS_186_plots_' + project + '.pdf') + + else: + print("The provided plot_type: ", plot_type, " is not supported by this plotting function") + +# def main(): +# # # #plotSBS("/Users/ebergstr/Desktop/AID/output/SBS/AID.SBS384.all", "/Users/ebergstr/Desktop/", "AID", '384', False, custom_text_upper=['Similarity to PCAWG: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7'], custom_text_bottom=['Stability: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7', 'Similarity to PCAWG: 0.9']) +# plotID("/Users/ebergstr/Desktop/BRCA/output/INDEL/BRCA.INDEL83.all", "/Users/ebergstr/Desktop/", "BRCA", '83', True, custom_text_upper=['Similarity to PCAWG: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7'], custom_text_middle=['Stability: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7', 'Similarity to PCAWG: 0.9'], custom_text_bottom=['Stability: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7', 'Similarity to PCAWG: 0.9']) +# # # plotDBS("/Users/ebergstr/Desktop/Mel/output/DINUC/Mel.DBS186.all", "/Users/ebergstr/Desktop/", "Mel", '186', False, custom_text_upper=['Similarity to PCAWG: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7'], custom_text_middle=['Stability: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7', 'Similarity to PCAWG: 0.9'], custom_text_bottom=['Stability: 0.98', 'Similarity to PCAWG: 0.9', 'Similarity to PCAWG: 0.7', 'Similarity to PCAWG: 0.9']) + +# # # # #plotSBS("/Users/ebergstr/Desktop/BRCA/output/SBS/BRCA.SBS1536.all", "/Users/ebergstr/Desktop/", "BRCA", '1536', False, custom_text_upper=['Similarity to PCAWG: 0.98'], custom_text_middle= ['Similarity to PCAWG: 0.98'], custom_text_bottom=['Stability: 0.98']) +# # # #plotSBS("/Users/ebergstr/Desktop/BRCA/output/SBS/BRCA.SBS1536.all", "/Users/ebergstr/Desktop/", "BRCA", '1536', False, custom_text_upper=['Similarity to PCAWG: 0.98'], custom_text_middle= ['Similarity to PCAWG: 0.98']) + +# # # # plotDBS("/Users/ebergstr/Downloads/Biliary-AdenoCA.dinucs.csv", "/Users/ebergstr/Desktop/", "test", '78', False) + +# if __name__ == '__main__': +# main() diff --git a/SigProfilerAssignment/src/Accolade_fermante.png b/SigProfilerAssignment/DecompositionPlots/reference_files/Accolade_fermante.png similarity index 100% rename from SigProfilerAssignment/src/Accolade_fermante.png rename to SigProfilerAssignment/DecompositionPlots/reference_files/Accolade_fermante.png diff --git a/SigProfilerAssignment/src/CREDIT.md b/SigProfilerAssignment/DecompositionPlots/reference_files/CREDIT.md similarity index 100% rename from SigProfilerAssignment/src/CREDIT.md rename to SigProfilerAssignment/DecompositionPlots/reference_files/CREDIT.md diff --git a/SigProfilerAssignment/src/Fonts/Arial Bold.ttf b/SigProfilerAssignment/DecompositionPlots/reference_files/Fonts/Arial Bold.ttf similarity index 100% rename from SigProfilerAssignment/src/Fonts/Arial Bold.ttf rename to SigProfilerAssignment/DecompositionPlots/reference_files/Fonts/Arial Bold.ttf diff --git a/SigProfilerAssignment/data/cnvtest/all.breast.ascat.summary.sample.tsv b/SigProfilerAssignment/data/cnvtest/all.breast.ascat.summary.sample.tsv new file mode 100644 index 0000000..5b5299c --- /dev/null +++ b/SigProfilerAssignment/data/cnvtest/all.breast.ascat.summary.sample.tsv @@ -0,0 +1,10000 @@ +sample Chromosome Start Position End Position Normal TCN Normal BCN Tumour TCN Tumour BCN +PD9067a 1 61735 61059101 2 1 2 1 +PD9067a 1 61059259 61062474 2 1 5 2 +PD9067a 1 61063647 72508131 2 1 2 1 +PD9067a 1 72508263 74035041 2 1 3 1 +PD9067a 1 74036249 84193241 2 1 2 1 +PD9067a 1 84196920 84220236 2 1 3 2 +PD9067a 1 84220313 121482979 2 1 2 1 +PD9067a 1 143982530 229921768 2 1 3 1 +PD9067a 1 229921927 233148539 2 1 3 2 +PD9067a 1 233150270 244307426 2 1 3 1 +PD9067a 1 244307774 244382698 2 1 4 1 +PD9067a 1 244383838 249224388 2 1 3 1 +PD9067a 2 12784 51315283 2 1 2 1 +PD9067a 2 51316018 51457836 2 1 0 0 +PD9067a 2 51462697 83334521 2 1 2 1 +PD9067a 2 83334835 84615472 2 1 3 1 +PD9067a 2 84616498 89107369 2 1 2 1 +PD9067a 2 89109612 89902175 2 1 7 3 +PD9067a 2 89903423 168892418 2 1 2 1 +PD9067a 2 168892954 169027149 2 1 1 1 +PD9067a 2 169027284 243089456 2 1 2 1 +PD9067a 3 60345 97786424 2 1 2 1 +PD9067a 3 97786559 97787341 2 1 0 0 +PD9067a 3 97787686 104274366 2 1 2 1 +PD9067a 3 104274913 106564007 2 1 1 0 +PD9067a 3 106568040 168811465 2 1 2 1 +PD9067a 3 168811680 168815167 2 1 1 0 +PD9067a 3 168815209 197896118 2 1 2 1 +PD9067a 4 12281 24989939 2 1 1 0 +PD9067a 4 24991040 25045895 2 1 2 0 +PD9067a 4 25046241 35334492 2 1 1 0 +PD9067a 4 35340044 35349263 2 1 4 1 +PD9067a 4 35351232 35779491 2 1 1 0 +PD9067a 4 35780805 36424976 2 1 1 1 +PD9067a 4 36424996 39146735 2 1 1 0 +PD9067a 4 39147049 40901689 2 1 2 1 +PD9067a 4 40901694 42197890 2 1 1 0 +PD9067a 4 42201811 87254046 2 1 2 1 +PD9067a 4 87254874 87256310 2 1 0 0 +PD9067a 4 87256623 163057553 2 1 2 1 +PD9067a 4 163059187 163061755 2 1 0 0 +PD9067a 4 163061844 191027923 2 1 2 1 +PD9067a 5 15532 1186086 2 1 2 1 +PD9067a 5 1186121 1189456 2 1 6 3 +PD9067a 5 1190088 6392602 2 1 2 1 +PD9067a 5 6393448 6758971 2 1 2 0 +PD9067a 5 6759714 7967019 2 1 2 1 +PD9067a 5 7970137 7975171 2 1 7 4 +PD9067a 5 7975733 24972502 2 1 2 1 +PD9067a 5 24973020 24990295 2 1 5 3 +PD9067a 5 24993180 57309418 2 1 2 1 +PD9067a 5 57309750 57338357 2 1 13 6 +PD9067a 5 57340073 95882162 2 1 2 1 +PD9067a 5 95883462 95884094 2 1 0 0 +PD9067a 5 95884451 146030906 2 1 2 1 +PD9067a 5 146033044 146036835 2 1 5 3 +PD9067a 5 146037037 180790320 2 1 2 1 +PD9067a 6 149661 30252574 2 1 2 1 +PD9067a 6 30252836 30482993 2 1 1 1 +PD9067a 6 30512163 32736005 2 1 2 1 +PD9067a 6 32736103 32759252 2 1 0 0 +PD9067a 6 32759273 76170874 2 1 2 1 +PD9067a 6 76171241 77389236 2 1 1 0 +PD9067a 6 77390412 157986559 2 1 2 1 +PD9067a 6 157987617 158006856 2 1 5 2 +PD9067a 6 158012804 171051005 2 1 2 1 +PD9067a 7 43259 50542927 2 1 2 1 +PD9067a 7 50545093 50546261 2 1 0 0 +PD9067a 7 50546261 58019983 2 1 2 1 +PD9067a 7 61063974 64779334 2 1 1 0 +PD9067a 7 64781350 159127004 2 1 2 1 +PD9067a 8 31254 40314725 2 1 2 1 +PD9067a 8 40314789 40337783 2 1 3 2 +PD9067a 8 40337943 72943124 2 1 2 1 +PD9067a 8 72944154 72963135 2 1 1 0 +PD9067a 8 72964853 105217958 2 1 2 1 +PD9067a 8 105219400 105223774 2 1 0 0 +PD9067a 8 105224103 146298155 2 1 2 1 +PD9067a 9 37747 130843436 2 1 2 1 +PD9067a 9 130843882 130847230 2 1 0 0 +PD9067a 9 130847862 141091394 2 1 2 1 +PD9067a 10 72759 22189788 2 1 2 1 +PD9067a 10 22190655 22976560 2 1 2 0 +PD9067a 10 22982058 26929728 2 1 2 1 +PD9067a 10 26932699 26950590 2 1 1 0 +PD9067a 10 26950942 60888567 2 1 2 1 +PD9067a 10 60888902 61024357 2 1 3 1 +PD9067a 10 61024468 64675369 2 1 2 1 +PD9067a 10 64676260 64676640 2 1 0 0 +PD9067a 10 64677307 135506704 2 1 2 1 +PD9067a 11 198572 119990326 2 1 2 1 +PD9067a 11 119991166 120004713 2 1 5 2 +PD9067a 11 120005633 134944770 2 1 2 1 +PD9067a 12 150442 29147937 2 1 2 1 +PD9067a 12 29149089 31019564 2 1 1 0 +PD9067a 12 31023633 32644317 2 1 2 1 +PD9067a 12 32645059 34854498 2 1 2 0 +PD9067a 12 37857751 75033481 2 1 2 1 +PD9067a 12 75035619 75867565 2 1 1 0 +PD9067a 12 75867949 115358952 2 1 2 1 +PD9067a 12 115359424 115362508 2 1 7 3 +PD9067a 12 115363751 127717544 2 1 2 1 +PD9067a 12 127718715 127731714 2 1 5 2 +PD9067a 12 127732425 130206033 2 1 2 1 +PD9067a 12 130206702 130218412 2 1 1 0 +PD9067a 12 130220604 133778189 2 1 2 1 +PD9067a 13 19026949 115108397 2 1 2 1 +PD9067a 14 19002124 34083650 2 1 2 1 +PD9067a 14 34084149 34084773 2 1 0 0 +PD9067a 14 34085186 56962866 2 1 2 1 +PD9067a 14 56963072 56972779 2 1 1 0 +PD9067a 14 56974491 107285437 2 1 2 1 +PD9067a 15 20016328 29761195 2 1 2 1 +PD9067a 15 29761249 29764382 2 1 1 0 +PD9067a 15 29764531 48244146 2 1 2 1 +PD9067a 15 48244557 48940648 2 1 2 0 +PD9067a 15 48944538 76878362 2 1 2 1 +PD9067a 15 76891241 76895774 2 1 0 0 +PD9067a 15 76895775 98957941 2 1 2 1 +PD9067a 15 98958215 98969065 2 1 6 3 +PD9067a 15 98969618 102469040 2 1 2 1 +PD9067a 16 60777 32106967 2 1 2 1 +PD9067a 16 32113682 33241953 2 1 0 0 +PD9067a 16 33300894 35283226 2 1 1 1 +PD9067a 16 46463782 80243012 2 1 1 0 +PD9067a 16 80243096 80247062 2 1 4 1 +PD9067a 16 80247886 87686735 2 1 1 0 +PD9067a 16 87687216 87689561 2 1 4 1 +PD9067a 16 87690403 90287535 2 1 1 0 +PD9067a 17 526 15961993 2 1 1 0 +PD9067a 17 15968143 18289557 2 1 2 1 +PD9067a 17 18289655 20087652 2 1 1 0 +PD9067a 17 20088289 20920488 2 1 3 1 +PD9067a 17 20923147 22235650 2 1 1 0 +PD9067a 17 25270411 45855956 2 1 2 1 +PD9067a 17 45858836 45863591 2 1 4 2 +PD9067a 17 45864314 81049726 2 1 2 1 +PD9067a 18 48133 8787857 2 1 2 1 +PD9067a 18 8789077 8789233 2 1 7 3 +PD9067a 18 8789381 78015057 2 1 2 1 +PD9067a 19 90910 59097854 2 1 2 1 +PD9067a 20 61305 62956153 2 1 2 1 +PD9067a 21 10736871 48096957 2 1 2 1 +PD9067a 22 16052528 51234455 2 1 2 1 +PD9067a 23 119805 24597949 2 1 2 1 +PD9067a 23 24598500 24631286 2 1 0 0 +PD9067a 23 24631657 29401353 2 1 2 1 +PD9067a 23 29403666 29465999 2 1 3 1 +PD9067a 23 29466132 55368262 2 1 2 1 +PD9067a 23 55368839 55382061 2 1 5 3 +PD9067a 23 55390370 97019201 2 1 2 1 +PD9067a 23 97019326 97026417 2 1 6 2 +PD9067a 23 97026853 110142047 2 1 2 1 +PD9067a 23 110145638 111530456 2 1 2 0 +PD9067a 23 111530530 115428847 2 1 2 1 +PD9067a 23 115429097 115460686 2 1 4 2 +PD9067a 23 115465397 155182354 2 1 2 1 +PD9067a 24 2649553 59033810 0 0 0 0 +PD24327a 1 564621 8320045 2 1 2 1 +PD24327a 1 8325842 8337974 2 1 3 1 +PD24327a 1 8342712 8365950 2 1 2 1 +PD24327a 1 8371186 14662281 2 1 3 1 +PD24327a 1 14662719 57291016 2 1 2 1 +PD24327a 1 57291133 109956851 2 1 3 1 +PD24327a 1 109968410 119256638 2 1 2 1 +PD24327a 1 119258848 121291080 2 1 3 1 +PD24327a 1 144538748 249198692 2 1 4 2 +PD24327a 2 15703 243048760 2 1 3 1 +PD24327a 3 69244 42875268 2 1 3 1 +PD24327a 3 42877075 60161647 2 1 1 0 +PD24327a 3 60162456 60723910 2 1 3 1 +PD24327a 3 60723969 60839058 2 1 1 0 +PD24327a 3 60841565 60972829 2 1 5 1 +PD24327a 3 60974088 79712954 2 1 1 0 +PD24327a 3 79712981 132544047 2 1 3 1 +PD24327a 3 132544206 140907784 2 1 4 1 +PD24327a 3 140910504 141081822 2 1 3 1 +PD24327a 3 141085972 142164017 2 1 5 1 +PD24327a 3 142178144 143139592 2 1 4 1 +PD24327a 3 143140428 147058937 2 1 5 1 +PD24327a 3 147059334 148895051 2 1 4 1 +PD24327a 3 148895126 197856433 2 1 5 1 +PD24327a 4 45410 20582119 2 1 3 1 +PD24327a 4 20594904 25987863 2 1 4 2 +PD24327a 4 25987977 46961617 2 1 3 1 +PD24327a 4 46961898 48498290 2 1 4 2 +PD24327a 4 48506163 60040672 2 1 3 1 +PD24327a 4 60040866 75201419 2 1 4 2 +PD24327a 4 75201884 136263707 2 1 3 1 +PD24327a 4 136280487 137498913 2 1 2 1 +PD24327a 4 137500406 140664557 2 1 3 1 +PD24327a 4 140668096 147754819 2 1 2 1 +PD24327a 4 147764571 148840417 2 1 3 1 +PD24327a 4 148847599 152989410 2 1 4 2 +PD24327a 4 152989476 161068083 2 1 3 1 +PD24327a 4 161094977 163391890 2 1 4 2 +PD24327a 4 163391920 185531630 2 1 3 1 +PD24327a 4 185532342 190921709 2 1 2 1 +PD24327a 5 36344 38935244 2 1 3 1 +PD24327a 5 38938664 41705432 2 1 4 2 +PD24327a 5 41710790 180692833 2 1 3 1 +PD24327a 6 203249 1232603 2 1 9 1 +PD24327a 6 1232932 1790238 2 1 11 1 +PD24327a 6 1795549 2646245 2 1 8 1 +PD24327a 6 2651987 2689064 2 1 4 0 +PD24327a 6 2696213 3665453 2 1 2 1 +PD24327a 6 3665573 4125941 2 1 4 1 +PD24327a 6 4126097 4163353 2 1 3 1 +PD24327a 6 4163436 6658043 2 1 2 1 +PD24327a 6 6659295 8961634 2 1 1 0 +PD24327a 6 8964270 9137281 2 1 8 1 +PD24327a 6 9138310 10842660 2 1 10 1 +PD24327a 6 10850468 11145945 2 1 18 1 +PD24327a 6 11146875 12226686 2 1 10 1 +PD24327a 6 12229938 12491467 2 1 9 1 +PD24327a 6 12501730 12638749 2 1 6 1 +PD24327a 6 12644940 13853160 2 1 2 1 +PD24327a 6 13863733 14062176 2 1 5 1 +PD24327a 6 14071732 14346355 2 1 11 1 +PD24327a 6 14347838 14354280 2 1 15 2 +PD24327a 6 14354851 14899485 2 1 16 1 +PD24327a 6 14904194 14949282 2 1 7 0 +PD24327a 6 14949328 15251181 2 1 8 1 +PD24327a 6 15256571 15873122 2 1 12 1 +PD24327a 6 15873951 15923323 2 1 7 0 +PD24327a 6 15923485 16340776 2 1 8 1 +PD24327a 6 16358358 16468304 2 1 2 0 +PD24327a 6 16471239 16777131 2 1 11 1 +PD24327a 6 16779951 17334641 2 1 14 1 +PD24327a 6 17339946 18321688 2 1 11 1 +PD24327a 6 18324635 18578438 2 1 5 1 +PD24327a 6 18579555 18936346 2 1 1 0 +PD24327a 6 18947638 20040950 2 1 10 1 +PD24327a 6 20041792 20346663 2 1 7 1 +PD24327a 6 20347670 20607684 2 1 13 1 +PD24327a 6 20611926 21220531 2 1 16 1 +PD24327a 6 21222751 22278396 2 1 20 1 +PD24327a 6 22280214 22643134 2 1 17 1 +PD24327a 6 22643749 22922468 2 1 10 0 +PD24327a 6 22926459 25291776 2 1 16 1 +PD24327a 6 25300739 25643792 2 1 10 1 +PD24327a 6 25645314 26663478 2 1 15 1 +PD24327a 6 26682323 27114052 2 1 3 1 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90420740 2 1 1 0 +PD11395a 13 90423877 102202289 2 1 2 1 diff --git a/SigProfilerAssignment/decompose_sub_routines.py b/SigProfilerAssignment/decompose_subroutines.py similarity index 100% rename from SigProfilerAssignment/decompose_sub_routines.py rename to SigProfilerAssignment/decompose_subroutines.py diff --git a/SigProfilerAssignment/decomposition.py b/SigProfilerAssignment/decomposition.py index 541b6c7..6141769 100644 --- a/SigProfilerAssignment/decomposition.py +++ b/SigProfilerAssignment/decomposition.py @@ -11,17 +11,18 @@ from cmath import cos # from torch import sign -from SigProfilerAssignment import decompose_sub_routines as sub +from SigProfilerAssignment import decompose_subroutines as sub import numpy as np import pandas as pd import SigProfilerMatrixGenerator from SigProfilerMatrixGenerator.scripts import SigProfilerMatrixGeneratorFunc as datadump +from SigProfilerMatrixGenerator.scripts import CNVMatrixGenerator as scna #import SigProfilerExtractor as cosmic import os,sys -def spa_analyze( samples, output,input_type='matrix',context_type="96", signatures=None, signature_database=None,decompose_fit_option= True,denovo_refit_option=True,cosmic_fit_option=True, nnls_add_penalty=0.05, +def spa_analyze(samples, output, input_type='matrix', context_type="96", signatures=None, signature_database=None,decompose_fit_option= True,denovo_refit_option=True,cosmic_fit_option=True, nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05, de_novo_fit_penalty=0.02, genome_build="GRCh37", cosmic_version=3.3, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8, exclude_signature_subgroups=None, exome=False): @@ -79,10 +80,16 @@ def spa_analyze( samples, output,input_type='matrix',context_type="96", signat if input_type=="vcf": project_name = 'Input_vcffiles' vcf_context = context_type - data = datadump.SigProfilerMatrixGeneratorFunc(project_name, genome_build, samples, exome=exome, bed_file=None, chrom_based=False, plot=False, gs=False) + data = datadump.SigProfilerMatrixGeneratorFunc(project_name, genome_build, samples, exome=exome, bed_file=None, chrom_based=False, plot=False, gs=False) genomes = data[vcf_context] - - elif input_type=="matrix": + + elif input_type.split(":")[0].lower()=="seg": + cnv_file_type = input_type.split(":")[1].upper() + context_type = "CNV48" + genomes = scna.generateCNVMatrix(cnv_file_type, samples, cnv_file_type, os.path.dirname(samples) + '/') + genomes = genomes.set_index('MutationType') + + elif input_type=="matrix": try: genomes = pd.read_csv(samples, sep = "\t", index_col = 0) except: @@ -197,7 +204,6 @@ def spa_analyze( samples, output,input_type='matrix',context_type="96", signat signature_names = sub.make_letter_ids(idlenth = processAvg.shape[1], mtype = mutation_context) # create the folder for the final solution/ De Novo Solution - #pdb.set_trace() exposureAvg_dummy = pd.DataFrame(np.random.rand(processAvg.shape[1],genomes.shape[1]),index=listOfSignatures,columns=colnames.to_list()).transpose().rename_axis('Samples') exposureAvg = exposureAvg_dummy exposureAvg.columns=signature_names @@ -433,8 +439,6 @@ def spa_analyze( samples, output,input_type='matrix',context_type="96", signat # # processAvg.drop(sig_exclusion_list, axis=1, inplace=True,errors='ignore') - # import pdb - # pdb.set_trace() #processAvg= originalProcessAvg #index = genomes.index #colnames = genomes.columns @@ -444,7 +448,6 @@ def spa_analyze( samples, output,input_type='matrix',context_type="96", signat for i in allsigids: attribution[i]= [i] #only for SBS96 - # pdb.set_trace() if mutation_type == "96" or mutation_type=="288" or mutation_type=="1536": background_sigs = sub.get_indeces(list(allsigids), ['SBS1', 'SBS5']) # add connected signatures @@ -459,8 +462,6 @@ def spa_analyze( samples, output,input_type='matrix',context_type="96", signat if genomes.shape[0] == processAvg.shape[0] and collapse_to_SBS96 ==True: sys.exit("Signatures Database and Samples are of same context type and is not equal to 96. please rerun by setting the flag \"collapse_to_SBS96 = False \"") - # import pdb - # pdb.set_trace() sub.make_final_solution(processAvg, genomes, allsigids, layer_directory3, mutation_type, index, colnames, diff --git a/SigProfilerAssignment/src/figures/SigProfilerAssignment.png b/SigProfilerAssignment/figures/SigProfilerAssignment.png similarity index 100% rename from SigProfilerAssignment/src/figures/SigProfilerAssignment.png rename to SigProfilerAssignment/figures/SigProfilerAssignment.png diff --git a/SigProfilerAssignment/src/figures/cosmic_fit.jpg b/SigProfilerAssignment/figures/cosmic_fit.jpg similarity index 100% rename from SigProfilerAssignment/src/figures/cosmic_fit.jpg rename to SigProfilerAssignment/figures/cosmic_fit.jpg diff --git a/SigProfilerAssignment/src/figures/cosmic_pic.jpg b/SigProfilerAssignment/figures/cosmic_pic.jpg similarity index 100% rename from SigProfilerAssignment/src/figures/cosmic_pic.jpg rename to SigProfilerAssignment/figures/cosmic_pic.jpg diff --git a/SigProfilerAssignment/src/figures/decomp_pic.jpg b/SigProfilerAssignment/figures/decomp_pic.jpg similarity index 100% rename from SigProfilerAssignment/src/figures/decomp_pic.jpg rename to SigProfilerAssignment/figures/decomp_pic.jpg diff --git a/SigProfilerAssignment/src/figures/denovo_fit.jpg b/SigProfilerAssignment/figures/denovo_fit.jpg similarity index 100% rename from SigProfilerAssignment/src/figures/denovo_fit.jpg rename to SigProfilerAssignment/figures/denovo_fit.jpg diff --git a/SigProfilerAssignment/single_sample.py b/SigProfilerAssignment/single_sample.py index 2bb95eb..ad98c7c 100644 --- a/SigProfilerAssignment/single_sample.py +++ b/SigProfilerAssignment/single_sample.py @@ -9,8 +9,7 @@ from numpy import linalg as LA from scipy.optimize import nnls from scipy.optimize import minimize -#from SigProfilerExtractor import subroutines as sub -from SigProfilerAssignment import decompose_sub_routines as sub +from SigProfilerAssignment import decompose_subroutines as sub import scipy.stats import copy import os diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS1248.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS1248.all deleted file mode 100644 index 00af893..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS1248.all +++ /dev/null @@ -1,1249 +0,0 @@ -MutationType -A[AC>CA]A -A[AC>CA]C -A[AC>CA]G -A[AC>CA]T -A[AC>CG]A -A[AC>CG]C -A[AC>CG]G -A[AC>CG]T -A[AC>CT]A -A[AC>CT]C -A[AC>CT]G -A[AC>CT]T -A[AC>GA]A -A[AC>GA]C -A[AC>GA]G -A[AC>GA]T -A[AC>GG]A -A[AC>GG]C -A[AC>GG]G -A[AC>GG]T -A[AC>GT]A -A[AC>GT]C -A[AC>GT]G -A[AC>GT]T -A[AC>TA]A -A[AC>TA]C -A[AC>TA]G -A[AC>TA]T -A[AC>TG]A -A[AC>TG]C -A[AC>TG]G -A[AC>TG]T -A[AC>TT]A -A[AC>TT]C -A[AC>TT]G -A[AC>TT]T -A[AT>CA]A -A[AT>CA]C -A[AT>CA]G -A[AT>CA]T -A[AT>CC]A -A[AT>CC]C -A[AT>CC]G -A[AT>CC]T -A[AT>CG]A -A[AT>CG]C -A[AT>CG]G -A[AT>CG]T -A[AT>GA]A -A[AT>GA]C -A[AT>GA]G -A[AT>GA]T -A[AT>GC]A -A[AT>GC]C -A[AT>GC]G -A[AT>GC]T -A[AT>TA]A -A[AT>TA]C -A[AT>TA]G -A[AT>TA]T -A[CC>AA]A -A[CC>AA]C -A[CC>AA]G -A[CC>AA]T -A[CC>AG]A -A[CC>AG]C -A[CC>AG]G -A[CC>AG]T -A[CC>AT]A -A[CC>AT]C -A[CC>AT]G -A[CC>AT]T -A[CC>GA]A -A[CC>GA]C -A[CC>GA]G -A[CC>GA]T -A[CC>GG]A -A[CC>GG]C -A[CC>GG]G -A[CC>GG]T -A[CC>GT]A -A[CC>GT]C -A[CC>GT]G -A[CC>GT]T -A[CC>TA]A -A[CC>TA]C -A[CC>TA]G -A[CC>TA]T -A[CC>TG]A -A[CC>TG]C -A[CC>TG]G -A[CC>TG]T -A[CC>TT]A -A[CC>TT]C -A[CC>TT]G -A[CC>TT]T -A[CG>AT]A -A[CG>AT]C -A[CG>AT]G -A[CG>AT]T -A[CG>GC]A -A[CG>GC]C -A[CG>GC]G -A[CG>GC]T -A[CG>GT]A -A[CG>GT]C -A[CG>GT]G -A[CG>GT]T -A[CG>TA]A -A[CG>TA]C -A[CG>TA]G -A[CG>TA]T -A[CG>TC]A -A[CG>TC]C -A[CG>TC]G -A[CG>TC]T -A[CG>TT]A -A[CG>TT]C -A[CG>TT]G -A[CG>TT]T -A[CT>AA]A -A[CT>AA]C -A[CT>AA]G -A[CT>AA]T -A[CT>AC]A -A[CT>AC]C -A[CT>AC]G -A[CT>AC]T -A[CT>AG]A -A[CT>AG]C -A[CT>AG]G -A[CT>AG]T -A[CT>GA]A -A[CT>GA]C -A[CT>GA]G -A[CT>GA]T -A[CT>GC]A 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-T[TA>GT]G -T[TA>GT]T -T[TC>AA]A -T[TC>AA]C -T[TC>AA]G -T[TC>AA]T -T[TC>AG]A -T[TC>AG]C -T[TC>AG]G -T[TC>AG]T -T[TC>AT]A -T[TC>AT]C -T[TC>AT]G -T[TC>AT]T -T[TC>CA]A -T[TC>CA]C -T[TC>CA]G -T[TC>CA]T -T[TC>CG]A -T[TC>CG]C -T[TC>CG]G -T[TC>CG]T -T[TC>CT]A -T[TC>CT]C -T[TC>CT]G -T[TC>CT]T -T[TC>GA]A -T[TC>GA]C -T[TC>GA]G -T[TC>GA]T -T[TC>GG]A -T[TC>GG]C -T[TC>GG]G -T[TC>GG]T -T[TC>GT]A -T[TC>GT]C -T[TC>GT]G -T[TC>GT]T -T[TG>AA]A -T[TG>AA]C -T[TG>AA]G -T[TG>AA]T -T[TG>AC]A -T[TG>AC]C -T[TG>AC]G -T[TG>AC]T -T[TG>AT]A -T[TG>AT]C -T[TG>AT]G -T[TG>AT]T -T[TG>CA]A -T[TG>CA]C -T[TG>CA]G -T[TG>CA]T -T[TG>CC]A -T[TG>CC]C -T[TG>CC]G -T[TG>CC]T -T[TG>CT]A -T[TG>CT]C -T[TG>CT]G -T[TG>CT]T -T[TG>GA]A -T[TG>GA]C -T[TG>GA]G -T[TG>GA]T -T[TG>GC]A -T[TG>GC]C -T[TG>GC]G -T[TG>GC]T -T[TG>GT]A -T[TG>GT]C -T[TG>GT]G -T[TG>GT]T -T[TT>AA]A -T[TT>AA]C -T[TT>AA]G -T[TT>AA]T -T[TT>AC]A -T[TT>AC]C -T[TT>AC]G -T[TT>AC]T -T[TT>AG]A -T[TT>AG]C -T[TT>AG]G -T[TT>AG]T -T[TT>CA]A -T[TT>CA]C -T[TT>CA]G -T[TT>CA]T -T[TT>CC]A -T[TT>CC]C -T[TT>CC]G -T[TT>CC]T -T[TT>CG]A -T[TT>CG]C -T[TT>CG]G -T[TT>CG]T -T[TT>GA]A -T[TT>GA]C -T[TT>GA]G -T[TT>GA]T -T[TT>GC]A -T[TT>GC]C -T[TT>GC]G -T[TT>GC]T -T[TT>GG]A -T[TT>GG]C -T[TT>GG]G -T[TT>GG]T \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS186.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS186.all deleted file mode 100644 index aaac04f..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS186.all +++ /dev/null @@ -1,187 +0,0 @@ -MutationType -T:CC>AA -T:CC>AG -T:CC>AT -T:CC>GA -T:CC>GG -T:CC>GT -T:CC>TA -T:CC>TG -T:CC>TT -T:CT>AA -T:CT>AC -T:CT>AG -T:CT>GA -T:CT>GC -T:CT>GG -T:CT>TA -T:CT>TC -T:CT>TG -T:TC>AA -T:TC>AG -T:TC>AT -T:TC>CA -T:TC>CG -T:TC>CT -T:TC>GA -T:TC>GG -T:TC>GT -T:TT>AA -T:TT>AC -T:TT>AG -T:TT>CA -T:TT>CC -T:TT>CG -T:TT>GA -T:TT>GC -T:TT>GG -U:CC>AA -U:CC>AG -U:CC>AT -U:CC>GA -U:CC>GG -U:CC>GT -U:CC>TA -U:CC>TG -U:CC>TT -U:CT>AA -U:CT>AC -U:CT>AG -U:CT>GA -U:CT>GC -U:CT>GG -U:CT>TA -U:CT>TC -U:CT>TG -U:TC>AA -U:TC>AG -U:TC>AT -U:TC>CA -U:TC>CG -U:TC>CT -U:TC>GA -U:TC>GG -U:TC>GT -U:TT>AA -U:TT>AC -U:TT>AG -U:TT>CA -U:TT>CC -U:TT>CG -U:TT>GA -U:TT>GC -U:TT>GG -B:CC>AA -B:CC>AG -B:CC>AT -B:CC>GA -B:CC>GG -B:CC>GT -B:CC>TA -B:CC>TG -B:CC>TT -B:CT>AA -B:CT>AC -B:CT>AG -B:CT>GA -B:CT>GC -B:CT>GG -B:CT>TA -B:CT>TC -B:CT>TG -B:TC>AA -B:TC>AG -B:TC>AT -B:TC>CA -B:TC>CG -B:TC>CT -B:TC>GA -B:TC>GG -B:TC>GT -B:TT>AA -B:TT>AC -B:TT>AG -B:TT>CA -B:TT>CC -B:TT>CG -B:TT>GA -B:TT>GC -B:TT>GG -N:CC>AA -N:CC>AG -N:CC>AT -N:CC>GA -N:CC>GG -N:CC>GT -N:CC>TA -N:CC>TG -N:CC>TT -N:CT>AA -N:CT>AC -N:CT>AG -N:CT>GA -N:CT>GC -N:CT>GG -N:CT>TA -N:CT>TC -N:CT>TG -N:TC>AA -N:TC>AG -N:TC>AT -N:TC>CA -N:TC>CG -N:TC>CT -N:TC>GA -N:TC>GG -N:TC>GT -N:TT>AA -N:TT>AC -N:TT>AG -N:TT>CA -N:TT>CC -N:TT>CG -N:TT>GA -N:TT>GC -N:TT>GG -Q:AC>CA -Q:AC>CG -Q:AC>CT -Q:AC>GA -Q:AC>GG -Q:AC>GT -Q:AC>TA -Q:AC>TG -Q:AC>TT -Q:AT>CA -Q:AT>CC -Q:AT>CG -Q:AT>GA -Q:AT>GC -Q:AT>TA -Q:CG>AT -Q:CG>GC -Q:CG>GT -Q:CG>TA -Q:CG>TC -Q:CG>TT -Q:GC>AA -Q:GC>AG -Q:GC>AT -Q:GC>CA -Q:GC>CG -Q:GC>TA -Q:TA>AT -Q:TA>CG -Q:TA>CT -Q:TA>GC -Q:TA>GG -Q:TA>GT -Q:TG>AA -Q:TG>AC -Q:TG>AT -Q:TG>CA -Q:TG>CC -Q:TG>CT -Q:TG>GA -Q:TG>GC -Q:TG>GT \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS2976.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS2976.all deleted file mode 100644 index fd235b6..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS2976.all +++ /dev/null @@ -1,2977 +0,0 @@ -MutationType -T:A[CC>AA]A -T:A[CC>AA]C -T:A[CC>AA]G -T:A[CC>AA]T -T:A[CC>AG]A -T:A[CC>AG]C -T:A[CC>AG]G -T:A[CC>AG]T -T:A[CC>AT]A -T:A[CC>AT]C -T:A[CC>AT]G -T:A[CC>AT]T -T:A[CC>GA]A -T:A[CC>GA]C -T:A[CC>GA]G -T:A[CC>GA]T -T:A[CC>GG]A -T:A[CC>GG]C -T:A[CC>GG]G -T:A[CC>GG]T -T:A[CC>GT]A -T:A[CC>GT]C -T:A[CC>GT]G -T:A[CC>GT]T -T:A[CC>TA]A -T:A[CC>TA]C -T:A[CC>TA]G -T:A[CC>TA]T -T:A[CC>TG]A -T:A[CC>TG]C -T:A[CC>TG]G -T:A[CC>TG]T -T:A[CC>TT]A -T:A[CC>TT]C -T:A[CC>TT]G -T:A[CC>TT]T -T:A[CT>AA]A -T:A[CT>AA]C -T:A[CT>AA]G -T:A[CT>AA]T -T:A[CT>AC]A -T:A[CT>AC]C -T:A[CT>AC]G -T:A[CT>AC]T -T:A[CT>AG]A -T:A[CT>AG]C -T:A[CT>AG]G -T:A[CT>AG]T -T:A[CT>GA]A -T:A[CT>GA]C -T:A[CT>GA]G -T:A[CT>GA]T -T:A[CT>GC]A -T:A[CT>GC]C -T:A[CT>GC]G -T:A[CT>GC]T -T:A[CT>GG]A -T:A[CT>GG]C -T:A[CT>GG]G -T:A[CT>GG]T -T:A[CT>TA]A -T:A[CT>TA]C -T:A[CT>TA]G -T:A[CT>TA]T -T:A[CT>TC]A -T:A[CT>TC]C -T:A[CT>TC]G -T:A[CT>TC]T -T:A[CT>TG]A -T:A[CT>TG]C -T:A[CT>TG]G -T:A[CT>TG]T -T:A[TC>AA]A -T:A[TC>AA]C -T:A[TC>AA]G -T:A[TC>AA]T -T:A[TC>AG]A -T:A[TC>AG]C -T:A[TC>AG]G -T:A[TC>AG]T -T:A[TC>AT]A -T:A[TC>AT]C -T:A[TC>AT]G -T:A[TC>AT]T -T:A[TC>CA]A -T:A[TC>CA]C -T:A[TC>CA]G -T:A[TC>CA]T -T:A[TC>CG]A -T:A[TC>CG]C -T:A[TC>CG]G -T:A[TC>CG]T -T:A[TC>CT]A -T:A[TC>CT]C -T:A[TC>CT]G -T:A[TC>CT]T -T:A[TC>GA]A -T:A[TC>GA]C -T:A[TC>GA]G -T:A[TC>GA]T -T:A[TC>GG]A -T:A[TC>GG]C -T:A[TC>GG]G -T:A[TC>GG]T -T:A[TC>GT]A -T:A[TC>GT]C -T:A[TC>GT]G -T:A[TC>GT]T -T:A[TT>AA]A -T:A[TT>AA]C -T:A[TT>AA]G -T:A[TT>AA]T -T:A[TT>AC]A -T:A[TT>AC]C -T:A[TT>AC]G -T:A[TT>AC]T -T:A[TT>AG]A -T:A[TT>AG]C -T:A[TT>AG]G -T:A[TT>AG]T -T:A[TT>CA]A -T:A[TT>CA]C -T:A[TT>CA]G -T:A[TT>CA]T -T:A[TT>CC]A -T:A[TT>CC]C -T:A[TT>CC]G -T:A[TT>CC]T -T:A[TT>CG]A -T:A[TT>CG]C -T:A[TT>CG]G -T:A[TT>CG]T -T:A[TT>GA]A -T:A[TT>GA]C -T:A[TT>GA]G -T:A[TT>GA]T -T:A[TT>GC]A -T:A[TT>GC]C -T:A[TT>GC]G -T:A[TT>GC]T -T:A[TT>GG]A -T:A[TT>GG]C -T:A[TT>GG]G -T:A[TT>GG]T -T:C[CC>AA]A -T:C[CC>AA]C -T:C[CC>AA]G -T:C[CC>AA]T -T:C[CC>AG]A -T:C[CC>AG]C -T:C[CC>AG]G -T:C[CC>AG]T -T:C[CC>AT]A -T:C[CC>AT]C -T:C[CC>AT]G -T:C[CC>AT]T -T:C[CC>GA]A -T:C[CC>GA]C -T:C[CC>GA]G -T:C[CC>GA]T -T:C[CC>GG]A -T:C[CC>GG]C -T:C[CC>GG]G -T:C[CC>GG]T -T:C[CC>GT]A -T:C[CC>GT]C -T:C[CC>GT]G -T:C[CC>GT]T -T:C[CC>TA]A -T:C[CC>TA]C -T:C[CC>TA]G -T:C[CC>TA]T -T:C[CC>TG]A -T:C[CC>TG]C -T:C[CC>TG]G -T:C[CC>TG]T -T:C[CC>TT]A -T:C[CC>TT]C -T:C[CC>TT]G -T:C[CC>TT]T -T:C[CT>AA]A -T:C[CT>AA]C -T:C[CT>AA]G -T:C[CT>AA]T -T:C[CT>AC]A -T:C[CT>AC]C -T:C[CT>AC]G -T:C[CT>AC]T -T:C[CT>AG]A -T:C[CT>AG]C -T:C[CT>AG]G -T:C[CT>AG]T -T:C[CT>GA]A -T:C[CT>GA]C -T:C[CT>GA]G -T:C[CT>GA]T -T:C[CT>GC]A -T:C[CT>GC]C -T:C[CT>GC]G -T:C[CT>GC]T -T:C[CT>GG]A -T:C[CT>GG]C -T:C[CT>GG]G -T:C[CT>GG]T -T:C[CT>TA]A -T:C[CT>TA]C -T:C[CT>TA]G -T:C[CT>TA]T -T:C[CT>TC]A -T:C[CT>TC]C -T:C[CT>TC]G -T:C[CT>TC]T -T:C[CT>TG]A -T:C[CT>TG]C -T:C[CT>TG]G -T:C[CT>TG]T -T:C[TC>AA]A -T:C[TC>AA]C -T:C[TC>AA]G -T:C[TC>AA]T -T:C[TC>AG]A -T:C[TC>AG]C -T:C[TC>AG]G -T:C[TC>AG]T -T:C[TC>AT]A -T:C[TC>AT]C -T:C[TC>AT]G -T:C[TC>AT]T -T:C[TC>CA]A -T:C[TC>CA]C -T:C[TC>CA]G -T:C[TC>CA]T -T:C[TC>CG]A -T:C[TC>CG]C -T:C[TC>CG]G -T:C[TC>CG]T -T:C[TC>CT]A -T:C[TC>CT]C -T:C[TC>CT]G -T:C[TC>CT]T -T:C[TC>GA]A -T:C[TC>GA]C -T:C[TC>GA]G -T:C[TC>GA]T -T:C[TC>GG]A -T:C[TC>GG]C -T:C[TC>GG]G -T:C[TC>GG]T -T:C[TC>GT]A -T:C[TC>GT]C -T:C[TC>GT]G -T:C[TC>GT]T -T:C[TT>AA]A -T:C[TT>AA]C -T:C[TT>AA]G -T:C[TT>AA]T -T:C[TT>AC]A -T:C[TT>AC]C -T:C[TT>AC]G -T:C[TT>AC]T -T:C[TT>AG]A -T:C[TT>AG]C -T:C[TT>AG]G -T:C[TT>AG]T -T:C[TT>CA]A 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-Q:T[TG>CT]A -Q:T[TG>CT]C -Q:T[TG>CT]G -Q:T[TG>CT]T -Q:T[TG>GA]A -Q:T[TG>GA]C -Q:T[TG>GA]G -Q:T[TG>GA]T -Q:T[TG>GC]A -Q:T[TG>GC]C -Q:T[TG>GC]G -Q:T[TG>GC]T -Q:T[TG>GT]A -Q:T[TG>GT]C -Q:T[TG>GT]G -Q:T[TG>GT]T \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS78.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS78.all deleted file mode 100644 index f51ae84..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.DBS78.all +++ /dev/null @@ -1,79 +0,0 @@ -MutationType -AC>CA -AC>CG -AC>CT -AC>GA -AC>GG -AC>GT -AC>TA -AC>TG -AC>TT -AT>CA -AT>CC -AT>CG -AT>GA -AT>GC -AT>TA -CC>AA -CC>AG -CC>AT -CC>GA -CC>GG -CC>GT -CC>TA -CC>TG -CC>TT -CG>AT -CG>GC -CG>GT -CG>TA -CG>TC -CG>TT -CT>AA -CT>AC -CT>AG -CT>GA -CT>GC -CT>GG -CT>TA -CT>TC -CT>TG -GC>AA -GC>AG -GC>AT -GC>CA -GC>CG -GC>TA -TA>AT -TA>CG -TA>CT -TA>GC -TA>GG -TA>GT -TC>AA -TC>AG -TC>AT -TC>CA -TC>CG -TC>CT -TC>GA -TC>GG -TC>GT -TG>AA -TG>AC -TG>AT -TG>CA -TG>CC -TG>CT -TG>GA -TG>GC -TG>GT -TT>AA -TT>AC -TT>AG -TT>CA -TT>CC -TT>CG -TT>GA -TT>GC -TT>GG \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID28.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID28.all deleted file mode 100644 index d5c0a40..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID28.all +++ /dev/null @@ -1,29 +0,0 @@ -MutationType -1:Del:C:0 -1:Del:C:1 -1:Del:C:2 -1:Del:C:3 -1:Del:C:4 -1:Del:C:5 -1:Del:T:0 -1:Del:T:1 -1:Del:T:2 -1:Del:T:3 -1:Del:T:4 -1:Del:T:5 -1:Ins:C:0 -1:Ins:C:1 -1:Ins:C:2 -1:Ins:C:3 -1:Ins:C:4 -1:Ins:C:5 -1:Ins:T:0 -1:Ins:T:1 -1:Ins:T:2 -1:Ins:T:3 -1:Ins:T:4 -1:Ins:T:5 -long_Del -long_Ins -MH -complex \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID415.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID415.all deleted file mode 100644 index 1630949..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID415.all +++ /dev/null @@ -1,416 +0,0 @@ -MutationType -T:1:Del:C:0 -T:1:Del:C:1 -T:1:Del:C:2 -T:1:Del:C:3 -T:1:Del:C:4 -T:1:Del:C:5 -T:1:Del:T:0 -T:1:Del:T:1 -T:1:Del:T:2 -T:1:Del:T:3 -T:1:Del:T:4 -T:1:Del:T:5 -T:2:Del:R:0 -T:2:Del:R:1 -T:2:Del:R:2 -T:2:Del:R:3 -T:2:Del:R:4 -T:2:Del:R:5 -T:3:Del:R:0 -T:3:Del:R:1 -T:3:Del:R:2 -T:3:Del:R:3 -T:3:Del:R:4 -T:3:Del:R:5 -T:4:Del:R:0 -T:4:Del:R:1 -T:4:Del:R:2 -T:4:Del:R:3 -T:4:Del:R:4 -T:4:Del:R:5 -T:5:Del:R:0 -T:5:Del:R:1 -T:5:Del:R:2 -T:5:Del:R:3 -T:5:Del:R:4 -T:5:Del:R:5 -T:2:Del:M:1 -T:3:Del:M:1 -T:3:Del:M:2 -T:4:Del:M:1 -T:4:Del:M:2 -T:4:Del:M:3 -T:5:Del:M:1 -T:5:Del:M:2 -T:5:Del:M:3 -T:5:Del:M:4 -T:5:Del:M:5 -T:1:Ins:C:0 -T:1:Ins:C:1 -T:1:Ins:C:2 -T:1:Ins:C:3 -T:1:Ins:C:4 -T:1:Ins:C:5 -T:1:Ins:T:0 -T:1:Ins:T:1 -T:1:Ins:T:2 -T:1:Ins:T:3 -T:1:Ins:T:4 -T:1:Ins:T:5 -T:2:Ins:R:0 -T:2:Ins:R:1 -T:2:Ins:R:2 -T:2:Ins:R:3 -T:2:Ins:R:4 -T:2:Ins:R:5 -T:3:Ins:R:0 -T:3:Ins:R:1 -T:3:Ins:R:2 -T:3:Ins:R:3 -T:3:Ins:R:4 -T:3:Ins:R:5 -T:4:Ins:R:0 -T:4:Ins:R:1 -T:4:Ins:R:2 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-Q:1:Ins:C:3 -Q:1:Ins:C:4 -Q:1:Ins:C:5 -Q:1:Ins:T:0 -Q:1:Ins:T:1 -Q:1:Ins:T:2 -Q:1:Ins:T:3 -Q:1:Ins:T:4 -Q:1:Ins:T:5 -Q:2:Ins:R:0 -Q:2:Ins:R:1 -Q:2:Ins:R:2 -Q:2:Ins:R:3 -Q:2:Ins:R:4 -Q:2:Ins:R:5 -Q:3:Ins:R:0 -Q:3:Ins:R:1 -Q:3:Ins:R:2 -Q:3:Ins:R:3 -Q:3:Ins:R:4 -Q:3:Ins:R:5 -Q:4:Ins:R:0 -Q:4:Ins:R:1 -Q:4:Ins:R:2 -Q:4:Ins:R:3 -Q:4:Ins:R:4 -Q:4:Ins:R:5 -Q:5:Ins:R:0 -Q:5:Ins:R:1 -Q:5:Ins:R:2 -Q:5:Ins:R:3 -Q:5:Ins:R:4 -Q:5:Ins:R:5 \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID83.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID83.all deleted file mode 100644 index f255910..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.ID83.all +++ /dev/null @@ -1,84 +0,0 @@ -MutationType -1:Del:C:0 -1:Del:C:1 -1:Del:C:2 -1:Del:C:3 -1:Del:C:4 -1:Del:C:5 -1:Del:T:0 -1:Del:T:1 -1:Del:T:2 -1:Del:T:3 -1:Del:T:4 -1:Del:T:5 -1:Ins:C:0 -1:Ins:C:1 -1:Ins:C:2 -1:Ins:C:3 -1:Ins:C:4 -1:Ins:C:5 -1:Ins:T:0 -1:Ins:T:1 -1:Ins:T:2 -1:Ins:T:3 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a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS24.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS24.all deleted file mode 100644 index 3b5fed7..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS24.all +++ /dev/null @@ -1,25 +0,0 @@ -MutationType -T:C>A -T:C>G -T:C>T -T:T>A -T:T>C -T:T>G -U:C>A -U:C>G -U:C>T -U:T>A -U:T>C -U:T>G -B:C>A -B:C>G -B:C>T -B:T>A -B:T>C -B:T>G -N:C>A -N:C>G -N:C>T -N:T>A -N:T>C -N:T>G \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS384.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS384.all deleted file mode 100644 index 50f94bc..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS384.all +++ /dev/null @@ -1,385 +0,0 @@ -MutationType -T:A[C>A]A -T:A[C>A]C -T:A[C>A]G -T:A[C>A]T -T:A[C>G]A -T:A[C>G]C -T:A[C>G]G -T:A[C>G]T -T:A[C>T]A -T:A[C>T]C -T:A[C>T]G -T:A[C>T]T -T:A[T>A]A -T:A[T>A]C -T:A[T>A]G -T:A[T>A]T -T:A[T>C]A -T:A[T>C]C -T:A[T>C]G -T:A[T>C]T -T:A[T>G]A -T:A[T>G]C -T:A[T>G]G -T:A[T>G]T -T:C[C>A]A -T:C[C>A]C -T:C[C>A]G -T:C[C>A]T -T:C[C>G]A -T:C[C>G]C -T:C[C>G]G -T:C[C>G]T -T:C[C>T]A -T:C[C>T]C -T:C[C>T]G -T:C[C>T]T -T:C[T>A]A -T:C[T>A]C -T:C[T>A]G -T:C[T>A]T -T:C[T>C]A -T:C[T>C]C -T:C[T>C]G -T:C[T>C]T -T:C[T>G]A -T:C[T>G]C -T:C[T>G]G -T:C[T>G]T -T:G[C>A]A -T:G[C>A]C -T:G[C>A]G -T:G[C>A]T -T:G[C>G]A -T:G[C>G]C -T:G[C>G]G -T:G[C>G]T -T:G[C>T]A -T:G[C>T]C -T:G[C>T]G -T:G[C>T]T -T:G[T>A]A -T:G[T>A]C -T:G[T>A]G -T:G[T>A]T -T:G[T>C]A -T:G[T>C]C -T:G[T>C]G -T:G[T>C]T -T:G[T>G]A -T:G[T>G]C -T:G[T>G]G -T:G[T>G]T -T:T[C>A]A -T:T[C>A]C -T:T[C>A]G -T:T[C>A]T -T:T[C>G]A -T:T[C>G]C -T:T[C>G]G -T:T[C>G]T -T:T[C>T]A -T:T[C>T]C -T:T[C>T]G -T:T[C>T]T -T:T[T>A]A -T:T[T>A]C -T:T[T>A]G -T:T[T>A]T -T:T[T>C]A -T:T[T>C]C -T:T[T>C]G -T:T[T>C]T -T:T[T>G]A -T:T[T>G]C -T:T[T>G]G -T:T[T>G]T -U:A[C>A]A -U:A[C>A]C -U:A[C>A]G -U:A[C>A]T -U:A[C>G]A -U:A[C>G]C -U:A[C>G]G -U:A[C>G]T -U:A[C>T]A -U:A[C>T]C -U:A[C>T]G -U:A[C>T]T -U:A[T>A]A -U:A[T>A]C -U:A[T>A]G -U:A[T>A]T -U:A[T>C]A -U:A[T>C]C -U:A[T>C]G -U:A[T>C]T -U:A[T>G]A -U:A[T>G]C -U:A[T>G]G -U:A[T>G]T -U:C[C>A]A -U:C[C>A]C -U:C[C>A]G -U:C[C>A]T -U:C[C>G]A -U:C[C>G]C -U:C[C>G]G -U:C[C>G]T -U:C[C>T]A -U:C[C>T]C -U:C[C>T]G -U:C[C>T]T -U:C[T>A]A -U:C[T>A]C -U:C[T>A]G -U:C[T>A]T -U:C[T>C]A -U:C[T>C]C -U:C[T>C]G -U:C[T>C]T -U:C[T>G]A -U:C[T>G]C -U:C[T>G]G -U:C[T>G]T -U:G[C>A]A -U:G[C>A]C -U:G[C>A]G -U:G[C>A]T -U:G[C>G]A -U:G[C>G]C -U:G[C>G]G -U:G[C>G]T -U:G[C>T]A -U:G[C>T]C -U:G[C>T]G -U:G[C>T]T -U:G[T>A]A -U:G[T>A]C -U:G[T>A]G -U:G[T>A]T -U:G[T>C]A -U:G[T>C]C -U:G[T>C]G -U:G[T>C]T -U:G[T>G]A -U:G[T>G]C -U:G[T>G]G -U:G[T>G]T -U:T[C>A]A -U:T[C>A]C -U:T[C>A]G -U:T[C>A]T -U:T[C>G]A -U:T[C>G]C -U:T[C>G]G -U:T[C>G]T -U:T[C>T]A -U:T[C>T]C -U:T[C>T]G -U:T[C>T]T -U:T[T>A]A -U:T[T>A]C -U:T[T>A]G -U:T[T>A]T -U:T[T>C]A -U:T[T>C]C -U:T[T>C]G -U:T[T>C]T -U:T[T>G]A -U:T[T>G]C -U:T[T>G]G -U:T[T>G]T -B:A[C>A]A -B:A[C>A]C -B:A[C>A]G -B:A[C>A]T -B:A[C>G]A -B:A[C>G]C -B:A[C>G]G -B:A[C>G]T -B:A[C>T]A -B:A[C>T]C -B:A[C>T]G -B:A[C>T]T -B:A[T>A]A -B:A[T>A]C -B:A[T>A]G -B:A[T>A]T -B:A[T>C]A -B:A[T>C]C -B:A[T>C]G -B:A[T>C]T -B:A[T>G]A -B:A[T>G]C -B:A[T>G]G -B:A[T>G]T -B:C[C>A]A -B:C[C>A]C -B:C[C>A]G -B:C[C>A]T -B:C[C>G]A -B:C[C>G]C -B:C[C>G]G -B:C[C>G]T -B:C[C>T]A -B:C[C>T]C -B:C[C>T]G -B:C[C>T]T -B:C[T>A]A -B:C[T>A]C -B:C[T>A]G -B:C[T>A]T -B:C[T>C]A -B:C[T>C]C -B:C[T>C]G -B:C[T>C]T -B:C[T>G]A -B:C[T>G]C -B:C[T>G]G -B:C[T>G]T -B:G[C>A]A -B:G[C>A]C -B:G[C>A]G -B:G[C>A]T -B:G[C>G]A -B:G[C>G]C -B:G[C>G]G -B:G[C>G]T -B:G[C>T]A -B:G[C>T]C -B:G[C>T]G -B:G[C>T]T -B:G[T>A]A -B:G[T>A]C -B:G[T>A]G -B:G[T>A]T -B:G[T>C]A -B:G[T>C]C -B:G[T>C]G -B:G[T>C]T -B:G[T>G]A -B:G[T>G]C -B:G[T>G]G -B:G[T>G]T -B:T[C>A]A -B:T[C>A]C -B:T[C>A]G -B:T[C>A]T -B:T[C>G]A -B:T[C>G]C -B:T[C>G]G -B:T[C>G]T -B:T[C>T]A -B:T[C>T]C -B:T[C>T]G -B:T[C>T]T -B:T[T>A]A -B:T[T>A]C -B:T[T>A]G -B:T[T>A]T -B:T[T>C]A -B:T[T>C]C -B:T[T>C]G -B:T[T>C]T -B:T[T>G]A -B:T[T>G]C -B:T[T>G]G -B:T[T>G]T -N:A[C>A]A -N:A[C>A]C -N:A[C>A]G -N:A[C>A]T -N:A[C>G]A -N:A[C>G]C -N:A[C>G]G -N:A[C>G]T -N:A[C>T]A -N:A[C>T]C -N:A[C>T]G -N:A[C>T]T -N:A[T>A]A -N:A[T>A]C -N:A[T>A]G -N:A[T>A]T -N:A[T>C]A -N:A[T>C]C -N:A[T>C]G -N:A[T>C]T -N:A[T>G]A -N:A[T>G]C -N:A[T>G]G -N:A[T>G]T -N:C[C>A]A -N:C[C>A]C -N:C[C>A]G -N:C[C>A]T -N:C[C>G]A -N:C[C>G]C -N:C[C>G]G -N:C[C>G]T -N:C[C>T]A -N:C[C>T]C -N:C[C>T]G -N:C[C>T]T -N:C[T>A]A -N:C[T>A]C -N:C[T>A]G -N:C[T>A]T -N:C[T>C]A -N:C[T>C]C -N:C[T>C]G -N:C[T>C]T -N:C[T>G]A -N:C[T>G]C -N:C[T>G]G -N:C[T>G]T -N:G[C>A]A -N:G[C>A]C -N:G[C>A]G -N:G[C>A]T -N:G[C>G]A -N:G[C>G]C -N:G[C>G]G -N:G[C>G]T -N:G[C>T]A -N:G[C>T]C -N:G[C>T]G -N:G[C>T]T -N:G[T>A]A -N:G[T>A]C -N:G[T>A]G -N:G[T>A]T -N:G[T>C]A -N:G[T>C]C -N:G[T>C]G -N:G[T>C]T -N:G[T>G]A -N:G[T>G]C -N:G[T>G]G -N:G[T>G]T -N:T[C>A]A -N:T[C>A]C -N:T[C>A]G -N:T[C>A]T -N:T[C>G]A -N:T[C>G]C -N:T[C>G]G -N:T[C>G]T -N:T[C>T]A -N:T[C>T]C -N:T[C>T]G -N:T[C>T]T -N:T[T>A]A -N:T[T>A]C -N:T[T>A]G -N:T[T>A]T -N:T[T>C]A -N:T[T>C]C -N:T[T>C]G -N:T[T>C]T -N:T[T>G]A -N:T[T>G]C -N:T[T>G]G -N:T[T>G]T \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6.all deleted file mode 100644 index 2333fa0..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6.all +++ /dev/null @@ -1,7 +0,0 @@ -MutationType -C>A -C>G -C>T -T>A -T>C -T>G \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6144.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6144.all deleted file mode 100644 index 19b97d8..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS6144.all +++ /dev/null @@ -1,6145 +0,0 @@ -MutationType -T:AA[C>A]AA -T:AA[C>A]AC -T:AA[C>A]AG -T:AA[C>A]AT -T:AA[C>A]CA -T:AA[C>A]CC -T:AA[C>A]CG -T:AA[C>A]CT -T:AA[C>A]GA -T:AA[C>A]GC -T:AA[C>A]GG -T:AA[C>A]GT -T:AA[C>A]TA -T:AA[C>A]TC -T:AA[C>A]TG -T:AA[C>A]TT -T:AA[C>G]AA -T:AA[C>G]AC -T:AA[C>G]AG -T:AA[C>G]AT -T:AA[C>G]CA -T:AA[C>G]CC -T:AA[C>G]CG 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-N:GG[T>C]TA -N:GG[T>C]TC -N:GG[T>C]TG -N:GG[T>C]TT -N:GG[T>G]AA -N:GG[T>G]AC -N:GG[T>G]AG -N:GG[T>G]AT -N:GG[T>G]CA -N:GG[T>G]CC -N:GG[T>G]CG -N:GG[T>G]CT -N:GG[T>G]GA -N:GG[T>G]GC -N:GG[T>G]GG -N:GG[T>G]GT -N:GG[T>G]TA -N:GG[T>G]TC -N:GG[T>G]TG -N:GG[T>G]TT -N:GT[C>A]AA -N:GT[C>A]AC -N:GT[C>A]AG -N:GT[C>A]AT -N:GT[C>A]CA -N:GT[C>A]CC -N:GT[C>A]CG -N:GT[C>A]CT -N:GT[C>A]GA -N:GT[C>A]GC -N:GT[C>A]GG -N:GT[C>A]GT -N:GT[C>A]TA -N:GT[C>A]TC -N:GT[C>A]TG -N:GT[C>A]TT -N:GT[C>G]AA -N:GT[C>G]AC -N:GT[C>G]AG -N:GT[C>G]AT -N:GT[C>G]CA -N:GT[C>G]CC -N:GT[C>G]CG -N:GT[C>G]CT -N:GT[C>G]GA -N:GT[C>G]GC -N:GT[C>G]GG -N:GT[C>G]GT -N:GT[C>G]TA -N:GT[C>G]TC -N:GT[C>G]TG -N:GT[C>G]TT -N:GT[C>T]AA -N:GT[C>T]AC -N:GT[C>T]AG -N:GT[C>T]AT -N:GT[C>T]CA -N:GT[C>T]CC -N:GT[C>T]CG -N:GT[C>T]CT -N:GT[C>T]GA -N:GT[C>T]GC -N:GT[C>T]GG -N:GT[C>T]GT -N:GT[C>T]TA -N:GT[C>T]TC -N:GT[C>T]TG -N:GT[C>T]TT -N:GT[T>A]AA -N:GT[T>A]AC -N:GT[T>A]AG -N:GT[T>A]AT -N:GT[T>A]CA -N:GT[T>A]CC -N:GT[T>A]CG -N:GT[T>A]CT -N:GT[T>A]GA -N:GT[T>A]GC -N:GT[T>A]GG -N:GT[T>A]GT -N:GT[T>A]TA -N:GT[T>A]TC -N:GT[T>A]TG -N:GT[T>A]TT -N:GT[T>C]AA -N:GT[T>C]AC -N:GT[T>C]AG -N:GT[T>C]AT -N:GT[T>C]CA -N:GT[T>C]CC -N:GT[T>C]CG -N:GT[T>C]CT -N:GT[T>C]GA -N:GT[T>C]GC -N:GT[T>C]GG -N:GT[T>C]GT -N:GT[T>C]TA -N:GT[T>C]TC -N:GT[T>C]TG -N:GT[T>C]TT -N:GT[T>G]AA -N:GT[T>G]AC -N:GT[T>G]AG -N:GT[T>G]AT -N:GT[T>G]CA -N:GT[T>G]CC -N:GT[T>G]CG -N:GT[T>G]CT -N:GT[T>G]GA -N:GT[T>G]GC -N:GT[T>G]GG -N:GT[T>G]GT -N:GT[T>G]TA -N:GT[T>G]TC -N:GT[T>G]TG -N:GT[T>G]TT -N:TA[C>A]AA -N:TA[C>A]AC -N:TA[C>A]AG -N:TA[C>A]AT -N:TA[C>A]CA -N:TA[C>A]CC -N:TA[C>A]CG -N:TA[C>A]CT -N:TA[C>A]GA -N:TA[C>A]GC -N:TA[C>A]GG -N:TA[C>A]GT -N:TA[C>A]TA -N:TA[C>A]TC -N:TA[C>A]TG -N:TA[C>A]TT -N:TA[C>G]AA -N:TA[C>G]AC -N:TA[C>G]AG -N:TA[C>G]AT -N:TA[C>G]CA -N:TA[C>G]CC -N:TA[C>G]CG -N:TA[C>G]CT -N:TA[C>G]GA -N:TA[C>G]GC -N:TA[C>G]GG -N:TA[C>G]GT -N:TA[C>G]TA -N:TA[C>G]TC -N:TA[C>G]TG -N:TA[C>G]TT -N:TA[C>T]AA -N:TA[C>T]AC -N:TA[C>T]AG -N:TA[C>T]AT -N:TA[C>T]CA -N:TA[C>T]CC -N:TA[C>T]CG -N:TA[C>T]CT -N:TA[C>T]GA -N:TA[C>T]GC -N:TA[C>T]GG -N:TA[C>T]GT -N:TA[C>T]TA -N:TA[C>T]TC -N:TA[C>T]TG -N:TA[C>T]TT -N:TA[T>A]AA -N:TA[T>A]AC -N:TA[T>A]AG -N:TA[T>A]AT -N:TA[T>A]CA -N:TA[T>A]CC -N:TA[T>A]CG -N:TA[T>A]CT -N:TA[T>A]GA -N:TA[T>A]GC -N:TA[T>A]GG -N:TA[T>A]GT -N:TA[T>A]TA -N:TA[T>A]TC -N:TA[T>A]TG -N:TA[T>A]TT -N:TA[T>C]AA -N:TA[T>C]AC -N:TA[T>C]AG -N:TA[T>C]AT -N:TA[T>C]CA -N:TA[T>C]CC -N:TA[T>C]CG -N:TA[T>C]CT -N:TA[T>C]GA -N:TA[T>C]GC -N:TA[T>C]GG -N:TA[T>C]GT -N:TA[T>C]TA -N:TA[T>C]TC -N:TA[T>C]TG -N:TA[T>C]TT -N:TA[T>G]AA -N:TA[T>G]AC -N:TA[T>G]AG -N:TA[T>G]AT -N:TA[T>G]CA -N:TA[T>G]CC -N:TA[T>G]CG -N:TA[T>G]CT -N:TA[T>G]GA -N:TA[T>G]GC -N:TA[T>G]GG -N:TA[T>G]GT -N:TA[T>G]TA -N:TA[T>G]TC -N:TA[T>G]TG -N:TA[T>G]TT -N:TC[C>A]AA -N:TC[C>A]AC -N:TC[C>A]AG -N:TC[C>A]AT -N:TC[C>A]CA -N:TC[C>A]CC -N:TC[C>A]CG -N:TC[C>A]CT -N:TC[C>A]GA -N:TC[C>A]GC -N:TC[C>A]GG -N:TC[C>A]GT -N:TC[C>A]TA -N:TC[C>A]TC -N:TC[C>A]TG -N:TC[C>A]TT -N:TC[C>G]AA -N:TC[C>G]AC -N:TC[C>G]AG -N:TC[C>G]AT -N:TC[C>G]CA -N:TC[C>G]CC -N:TC[C>G]CG -N:TC[C>G]CT -N:TC[C>G]GA -N:TC[C>G]GC -N:TC[C>G]GG -N:TC[C>G]GT -N:TC[C>G]TA -N:TC[C>G]TC -N:TC[C>G]TG -N:TC[C>G]TT -N:TC[C>T]AA -N:TC[C>T]AC -N:TC[C>T]AG -N:TC[C>T]AT -N:TC[C>T]CA -N:TC[C>T]CC -N:TC[C>T]CG -N:TC[C>T]CT -N:TC[C>T]GA -N:TC[C>T]GC -N:TC[C>T]GG -N:TC[C>T]GT -N:TC[C>T]TA -N:TC[C>T]TC -N:TC[C>T]TG -N:TC[C>T]TT -N:TC[T>A]AA -N:TC[T>A]AC -N:TC[T>A]AG -N:TC[T>A]AT -N:TC[T>A]CA -N:TC[T>A]CC -N:TC[T>A]CG -N:TC[T>A]CT -N:TC[T>A]GA -N:TC[T>A]GC -N:TC[T>A]GG -N:TC[T>A]GT -N:TC[T>A]TA -N:TC[T>A]TC -N:TC[T>A]TG -N:TC[T>A]TT -N:TC[T>C]AA -N:TC[T>C]AC -N:TC[T>C]AG -N:TC[T>C]AT -N:TC[T>C]CA -N:TC[T>C]CC -N:TC[T>C]CG -N:TC[T>C]CT -N:TC[T>C]GA -N:TC[T>C]GC -N:TC[T>C]GG -N:TC[T>C]GT -N:TC[T>C]TA -N:TC[T>C]TC -N:TC[T>C]TG -N:TC[T>C]TT -N:TC[T>G]AA -N:TC[T>G]AC -N:TC[T>G]AG -N:TC[T>G]AT -N:TC[T>G]CA -N:TC[T>G]CC -N:TC[T>G]CG -N:TC[T>G]CT -N:TC[T>G]GA -N:TC[T>G]GC -N:TC[T>G]GG -N:TC[T>G]GT -N:TC[T>G]TA -N:TC[T>G]TC -N:TC[T>G]TG -N:TC[T>G]TT -N:TG[C>A]AA -N:TG[C>A]AC -N:TG[C>A]AG -N:TG[C>A]AT -N:TG[C>A]CA -N:TG[C>A]CC -N:TG[C>A]CG -N:TG[C>A]CT -N:TG[C>A]GA -N:TG[C>A]GC -N:TG[C>A]GG -N:TG[C>A]GT -N:TG[C>A]TA -N:TG[C>A]TC -N:TG[C>A]TG -N:TG[C>A]TT -N:TG[C>G]AA -N:TG[C>G]AC -N:TG[C>G]AG -N:TG[C>G]AT -N:TG[C>G]CA -N:TG[C>G]CC -N:TG[C>G]CG -N:TG[C>G]CT -N:TG[C>G]GA -N:TG[C>G]GC -N:TG[C>G]GG -N:TG[C>G]GT -N:TG[C>G]TA -N:TG[C>G]TC -N:TG[C>G]TG -N:TG[C>G]TT -N:TG[C>T]AA -N:TG[C>T]AC -N:TG[C>T]AG -N:TG[C>T]AT -N:TG[C>T]CA -N:TG[C>T]CC -N:TG[C>T]CG -N:TG[C>T]CT -N:TG[C>T]GA -N:TG[C>T]GC -N:TG[C>T]GG -N:TG[C>T]GT -N:TG[C>T]TA -N:TG[C>T]TC -N:TG[C>T]TG -N:TG[C>T]TT -N:TG[T>A]AA -N:TG[T>A]AC -N:TG[T>A]AG -N:TG[T>A]AT -N:TG[T>A]CA -N:TG[T>A]CC -N:TG[T>A]CG -N:TG[T>A]CT -N:TG[T>A]GA -N:TG[T>A]GC -N:TG[T>A]GG -N:TG[T>A]GT -N:TG[T>A]TA -N:TG[T>A]TC -N:TG[T>A]TG -N:TG[T>A]TT -N:TG[T>C]AA -N:TG[T>C]AC -N:TG[T>C]AG -N:TG[T>C]AT -N:TG[T>C]CA -N:TG[T>C]CC -N:TG[T>C]CG -N:TG[T>C]CT -N:TG[T>C]GA -N:TG[T>C]GC -N:TG[T>C]GG -N:TG[T>C]GT -N:TG[T>C]TA -N:TG[T>C]TC -N:TG[T>C]TG -N:TG[T>C]TT -N:TG[T>G]AA -N:TG[T>G]AC -N:TG[T>G]AG -N:TG[T>G]AT -N:TG[T>G]CA -N:TG[T>G]CC -N:TG[T>G]CG -N:TG[T>G]CT -N:TG[T>G]GA -N:TG[T>G]GC -N:TG[T>G]GG -N:TG[T>G]GT -N:TG[T>G]TA -N:TG[T>G]TC -N:TG[T>G]TG -N:TG[T>G]TT -N:TT[C>A]AA -N:TT[C>A]AC -N:TT[C>A]AG -N:TT[C>A]AT -N:TT[C>A]CA -N:TT[C>A]CC -N:TT[C>A]CG -N:TT[C>A]CT -N:TT[C>A]GA -N:TT[C>A]GC -N:TT[C>A]GG -N:TT[C>A]GT -N:TT[C>A]TA -N:TT[C>A]TC -N:TT[C>A]TG -N:TT[C>A]TT -N:TT[C>G]AA -N:TT[C>G]AC -N:TT[C>G]AG -N:TT[C>G]AT -N:TT[C>G]CA -N:TT[C>G]CC -N:TT[C>G]CG -N:TT[C>G]CT -N:TT[C>G]GA -N:TT[C>G]GC -N:TT[C>G]GG -N:TT[C>G]GT -N:TT[C>G]TA -N:TT[C>G]TC -N:TT[C>G]TG -N:TT[C>G]TT -N:TT[C>T]AA -N:TT[C>T]AC -N:TT[C>T]AG -N:TT[C>T]AT -N:TT[C>T]CA -N:TT[C>T]CC -N:TT[C>T]CG -N:TT[C>T]CT -N:TT[C>T]GA -N:TT[C>T]GC -N:TT[C>T]GG -N:TT[C>T]GT -N:TT[C>T]TA -N:TT[C>T]TC -N:TT[C>T]TG -N:TT[C>T]TT -N:TT[T>A]AA -N:TT[T>A]AC -N:TT[T>A]AG -N:TT[T>A]AT -N:TT[T>A]CA -N:TT[T>A]CC -N:TT[T>A]CG -N:TT[T>A]CT -N:TT[T>A]GA -N:TT[T>A]GC -N:TT[T>A]GG -N:TT[T>A]GT -N:TT[T>A]TA -N:TT[T>A]TC -N:TT[T>A]TG -N:TT[T>A]TT -N:TT[T>C]AA -N:TT[T>C]AC -N:TT[T>C]AG -N:TT[T>C]AT -N:TT[T>C]CA -N:TT[T>C]CC -N:TT[T>C]CG -N:TT[T>C]CT -N:TT[T>C]GA -N:TT[T>C]GC -N:TT[T>C]GG -N:TT[T>C]GT -N:TT[T>C]TA -N:TT[T>C]TC -N:TT[T>C]TG -N:TT[T>C]TT -N:TT[T>G]AA -N:TT[T>G]AC -N:TT[T>G]AG -N:TT[T>G]AT -N:TT[T>G]CA -N:TT[T>G]CC -N:TT[T>G]CG -N:TT[T>G]CT -N:TT[T>G]GA -N:TT[T>G]GC -N:TT[T>G]GG -N:TT[T>G]GT -N:TT[T>G]TA -N:TT[T>G]TC -N:TT[T>G]TG -N:TT[T>G]TT \ No newline at end of file diff --git a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS96.all b/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS96.all deleted file mode 100644 index 2f67d1a..0000000 --- a/SigProfilerAssignment/src/FormatFiles/Sample_Files.SBS96.all +++ /dev/null @@ -1,97 +0,0 @@ -MutationType -A[C>A]A -A[C>A]C -A[C>A]G -A[C>A]T -A[C>G]A -A[C>G]C -A[C>G]G -A[C>G]T -A[C>T]A -A[C>T]C -A[C>T]G -A[C>T]T -A[T>A]A -A[T>A]C -A[T>A]G -A[T>A]T -A[T>C]A -A[T>C]C -A[T>C]G -A[T>C]T -A[T>G]A -A[T>G]C -A[T>G]G -A[T>G]T -C[C>A]A -C[C>A]C -C[C>A]G -C[C>A]T -C[C>G]A -C[C>G]C -C[C>G]G -C[C>G]T -C[C>T]A -C[C>T]C -C[C>T]G -C[C>T]T -C[T>A]A -C[T>A]C -C[T>A]G -C[T>A]T -C[T>C]A -C[T>C]C -C[T>C]G -C[T>C]T -C[T>G]A -C[T>G]C -C[T>G]G -C[T>G]T -G[C>A]A -G[C>A]C -G[C>A]G -G[C>A]T -G[C>G]A -G[C>G]C -G[C>G]G -G[C>G]T -G[C>T]A -G[C>T]C -G[C>T]G -G[C>T]T -G[T>A]A -G[T>A]C -G[T>A]G -G[T>A]T -G[T>C]A -G[T>C]C -G[T>C]G -G[T>C]T -G[T>G]A -G[T>G]C -G[T>G]G -G[T>G]T -T[C>A]A -T[C>A]C -T[C>A]G -T[C>A]T -T[C>G]A -T[C>G]C -T[C>G]G -T[C>G]T -T[C>T]A -T[C>T]C -T[C>T]G -T[C>T]T -T[T>A]A -T[T>A]C -T[T>A]G -T[T>A]T -T[T>C]A -T[T>C]C -T[T>C]G -T[T>C]T -T[T>G]A -T[T>G]C -T[T>G]G -T[T>G]T \ No newline at end of file diff --git a/setup.py b/setup.py index 2093636..697a0f4 100644 --- a/setup.py +++ b/setup.py @@ -6,7 +6,7 @@ if os.path.exists("dist"): shutil.rmtree("dist") -VERSION = '0.0.13' +VERSION = '0.0.14' with open('README.md') as f: long_description = f.read() @@ -17,7 +17,7 @@ def write_version_py(filename='SigProfilerAssignment/version.py'): # THIS FILE IS GENERATED FROM SigProfilerAssignment SETUP.PY short_version = '%(version)s' version = '%(version)s' -Update = 'Update COSMIC v3.3' +Update = '1. Add support for multi-sample segmentation files. 2. Move decomposition plots to SigProfilerAssignment.' """ fh = open(filename, 'w')