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Merge pull request #701 from ARTbio/ez_histo
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add xrefs bio.tools
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@drosofff
drosofff authored Nov 7, 2024
2 parents 99a9852 + 595f5c9 commit f8dffb8
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202 changes: 103 additions & 99 deletions tools/ez_histograms/ez_histograms.R
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Original file line number Diff line number Diff line change
Expand Up @@ -5,121 +5,125 @@ library(scales)
library(psych)
library(optparse)

options(show.error.messages = FALSE,
error = function() {
cat(geterrmessage(), file = stderr())
q("no", 1, FALSE)
}
options(
show.error.messages = FALSE,
error = function() {
cat(geterrmessage(), file = stderr())
q("no", 1, FALSE)
}
)

loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
warnings()

option_list <- list(
make_option(
c("-f", "--file"),
default = NA,
type = "character",
help = "Input file that contains count values to transform"
),
make_option(
c("-d", "--profile"),
default = "count",
type = "character",
help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]"
),
make_option(
"--xscale",
default = "cartesian",
type = "character",
help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
),
make_option(
"--yscale",
default = "cartesian",
type = "character",
help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
),
make_option(
c("-p", "--pdf"),
default = "histograms.pdf",
type = "character",
help = "Output pdf file name [default : '%default' ]"
),
make_option(
c("-s", "--summary"),
default = "summary.tsv",
type = "character",
help = "statistics summary file name [default : '%default' ]"
)
make_option(
c("-f", "--file"),
default = NA,
type = "character",
help = "Input file that contains count values to transform"
),
make_option(
c("-d", "--profile"),
default = "count",
type = "character",
help = "Whether y-axis shows absolute counts or density: 'count' or 'density' [default : '%default' ]"
),
make_option(
"--xscale",
default = "cartesian",
type = "character",
help = "Whether x-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
),
make_option(
"--yscale",
default = "cartesian",
type = "character",
help = "Whether y-axis is 'cartesian', 'log2' or 'log10' [default : '%default' ]"
),
make_option(
c("-p", "--pdf"),
default = "histograms.pdf",
type = "character",
help = "Output pdf file name [default : '%default' ]"
),
make_option(
c("-s", "--summary"),
default = "summary.tsv",
type = "character",
help = "statistics summary file name [default : '%default' ]"
)
)

opt <- parse_args(OptionParser(option_list = option_list),
args = commandArgs(trailingOnly = TRUE))
args = commandArgs(trailingOnly = TRUE)
)

plot_histograms <- function(mdata, profile = "count", xscale = "cartesian", yscale = "cartesian", bins = 30) {
if (profile == "count") {
# count histogram
p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +
geom_histogram(bins = bins) + theme(legend.position = "none")
if (xscale == "cartesian") {
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (profile == "count") {
# count histogram
p <- ggplot(mdata, aes(x = value, fill = variable, color = variable, y = after_stat(count)), show.legend = FALSE) +
geom_histogram(bins = bins) +
theme(legend.position = "none")
if (xscale == "cartesian") {
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
}
}
}
}
}
if (xscale == "log2") {
p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (xscale == "log2") {
p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
}
}
}
}
}
if (xscale == "log10") {
p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (xscale == "log10") {
p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (yscale == "log2") {
p <- p + scale_y_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
} else {
if (yscale == "log10") {
p <- p + scale_y_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
}
}
}
}
}
}

if (profile == "density") {
# density histogram
p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +
geom_density() + theme(legend.position = "none")
if (xscale == "log2") {
p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
}
if (xscale == "log10") {
p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
if (profile == "density") {
# density histogram
p <- ggplot(mdata, aes(x = value, fill = variable, color = variable)) +
geom_density() +
theme(legend.position = "none")
if (xscale == "log2") {
p <- p + scale_x_continuous(trans = "log2", labels = trans_format("log2", math_format(2^.x)))
}
if (xscale == "log10") {
p <- p + scale_x_continuous(trans = "log10", labels = trans_format("log10", math_format(10^.x)))
}
}
}
return(p)
return(p)
}

test_header <- function(file) {
data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)
if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {
return(TRUE)
} else {
return(FALSE)
}
data <- read.delim(file = file, header = FALSE, row.names = 1, nrows = 2)
if (all(is.na(as.numeric(data[1, seq_len(ncol(data))])))) {
return(TRUE)
} else {
return(FALSE)
}
}

##### prepare input data

data <- read.delim(file = opt$file, header = test_header(opt$file))
data <- data %>% select(where(is.numeric)) # remove non numeric columns
data <- data %>% select(where(is.numeric)) # remove non numeric columns
mdata <- melt(data)

##### main
Expand All @@ -132,23 +136,23 @@ p <- plot_histograms(mdata, profile = opt$profile, xscale = opt$xscale, bins = b
# determine optimal width for the graph
width <- length(data)
width <- case_when(
width == 1 ~ 14 / 3,
width == 2 ~ (2 / 3) * 14,
TRUE ~ 14
width == 1 ~ 14 / 3,
width == 2 ~ (2 / 3) * 14,
TRUE ~ 14
)
# determine optimal height for the graph
height <- length(data)
height <- case_when(
height <= 3 ~ 3,
height <= 6 ~ 6,
TRUE ~ (floor(height / 3) + 1) * 3
height <= 3 ~ 3,
height <= 6 ~ 6,
TRUE ~ (floor(height / 3) + 1) * 3
)
# determine optimal number of col for the graph
ncol <- length(data)
ncol <- case_when(
ncol == 1 ~ 1,
ncol == 2 ~ 2,
TRUE ~ 3
ncol == 1 ~ 1,
ncol == 2 ~ 2,
TRUE ~ 3
)
pdf(opt$pdf, width = width, height = height)
print(p + facet_wrap(~variable, ncol = ncol, scales = "free"))
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7 changes: 6 additions & 1 deletion tools/ez_histograms/ez_histograms.xml
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Original file line number Diff line number Diff line change
@@ -1,9 +1,14 @@
<tool id="ez_histograms" name="ez_histograms" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
<macros>
<token name="@TOOL_VERSION@">3.4.4</token>
<token name="@VERSION_SUFFIX@">1</token>
<token name="@VERSION_SUFFIX@">2</token>
<token name="@PROFILE@">23.0</token>
</macros>

<xrefs>
<xref type="bio.tools">ez_histograms</xref>
</xrefs>

<requirements>
<requirement type="package" version="3.4.4">r-ggplot2</requirement>
<requirement type="package" version="1.4.4">r-reshape2</requirement>
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