Fixed more bugs in plotting scripts.

ejohnson643 · Nov 7, 2021 · d7f3dfa · d7f3dfa
1 parent 170875c
commit d7f3dfa
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Showing 6 changed files with 667 additions and 24 deletions.
diff --git a/EMBEDR/embedr.py b/EMBEDR/embedr.py
@@ -245,6 +245,7 @@ def _validate_parameters_without_data(self):
         return
 
     def __str__(self):
+
         out_str = ""
         if self.verbose > 1:
             out_str += f"\n\n\tEMBEDR Class v{ev}\n" + 35 * "=" + "\n\n"
@@ -2636,24 +2637,27 @@ def sweep_lineplot(self, sweep_type='pvalues', metadata=None, labels=None,
         if (metadata is None) or (labels is None):
             from EMBEDR.plots.sweep_lineplots import sweep_lineplot
 
-            axis = sweep_lineplot(hp_values,
+            return sweep_lineplot(hp_values,
                                   values_dict,
                                   fig=fig,
                                   axis=axis,
-                                  # xticks=xticks,
-                                  xticklabels=xticklabels, **kwargs)
+                                  xticks=xticks,
+                                  xticklabels=xticklabels,
+                                  **kwargs)
 
         else:
             from EMBEDR.plots.sweep_lineplots import sweep_lineplot_byCat
-            axes = sweep_lineplot_byCat(hp_values,
+            return sweep_lineplot_byCat(hp_values,
                                         values_dict,
                                         metadata,
                                         labels,
                                         fig=fig,
-                                        # xticks=xticks,
+                                        xticks=xticks,
                                         xticklabels=xticklabels,
                                         **kwargs)
 
+
+
     def plot_embedding(self,
                        param_2_plot='optimal',
                        plot_type='pvalue',
@@ -2690,9 +2694,9 @@ def plot_embedding(self,
 
         perp = knn = None
         if self.sweep_type == 'perplexity':
-            perp = param_2_plot
+            perp = np.ones((self.n_samples)) * param_2_plot
         else:
-            knn = param_2_plot
+            knn = np.ones((self.n_samples)) * param_2_plot
 
         tmpEmb = EMBEDR(perplexity=perp,
                         n_neighbors=knn,

diff --git a/EMBEDR/plots/EMBEDR_Figure_01v1_DimRed_Zoology.py b/EMBEDR/plots/EMBEDR_Figure_01v1_DimRed_Zoology.py
@@ -214,7 +214,8 @@ def EMBEDR_Figure_01(X,
                             n_data_embed=1,
                             n_jobs=-1,
                             project_name=project_name,
-                            project_dir=project_dir)
+                            project_dir=project_dir,
+                            **EMBEDR_params)
             Y, _ = embObj.get_tSNE_embedding(X)
             kEff = human_round(embObj.kEff)
             title = f"t-SNE: " + r"$k_{Eff} \approx $" + f"{kEff:.0f}"

diff --git a/EMBEDR/plots/embedr_scatterplots.py b/EMBEDR/plots/embedr_scatterplots.py
@@ -20,6 +20,7 @@ def __init__(self,
                  labels,
                  log_labels=False,
                  axis=None,
+                 axis_kwds=None,
                  show_border=True,
                  scatter_sizes=3,
                  scatter_alpha=1,
@@ -32,6 +33,7 @@ def __init__(self,
                  yticks=None,
                  yticklabels=None,
                  ylabel=None,
+                 grid_kwds=None,
                  label_size=12,
                  plot_order=None,
                  title=None,
@@ -55,6 +57,7 @@ def __init__(self,
             self.labels = np.log10(self.labels)
 
         self.axis        = axis
+        self.axis_kwds   = {} if axis_kwds is None else axis_kwds.copy()
         self.show_border = show_border
 
         self.sct_s     = scatter_sizes
@@ -74,6 +77,8 @@ def __init__(self,
         self.ylabel      = ylabel
         self.label_size  = label_size
 
+        self.grid_kwds   = {} if grid_kwds is None else grid_kwds.copy()
+
         if plot_order is None:
             self.sort_idx = np.arange(self.n_samples)
         elif plot_order.lower() == 'asc':
@@ -107,10 +112,18 @@ def plot(self, **kwargs):
             self.fig = self.axis.figure
 
         spine_alpha = 1 if self.show_border else 0
-        self.axis = putl.make_border_axes(self.axis, spine_alpha=spine_alpha)
+        self.axis = putl.make_border_axes(self.axis,
+                                          spine_alpha=spine_alpha,
+                                          xticks=self.xticks,
+                                          yticks=self.yticks,
+                                          xticklabels=self.xticklabels,
+                                          yticklabels=self.xticklabels,
+                                          **self.axis_kwds)
 
         self.axis = self._plot(**kwargs)
 
+        self.axis.grid(**self.grid_kwds)
+
         if self.cite_EMBEDR:
             if 'transform' not in self.text_kwds:
                 self.text_kwds['transform'] = self.axis.transAxes
@@ -261,8 +274,6 @@ def __init__(self, Y, label, metadata, **kwargs):
         if self.cmap is None:
             self.cmap = 'husl'
 
-        print(self.category_kwds)
-
         out = putl.process_categorical_label(metadata,
                                              label,
                                              cmap=self.cmap,
@@ -285,8 +296,6 @@ def _plot(self, **kwargs):
 
             good_idx = self._labels == label
             n_labs = sum(good_idx)
-            # if verbose:
-            #     print(f"There are {n_labs} samples with label = {label}")
 
             if label in self.labels_2_show:
 

diff --git a/EMBEDR/plots/sweep_boxplots.py b/EMBEDR/plots/sweep_boxplots.py
@@ -9,6 +9,7 @@
 class SweepBoxplot(object):
 
     BOX_PATCHES = ['boxes', 'whiskers', 'fliers', 'caps', 'medians']
+    GRID_KWDS = dict()
 
     def __init__(self,
                  hyperparam_array,
@@ -23,6 +24,7 @@ def __init__(self,
                  back_wpad=0.0,
                  back_hpad=0.0,
                  fig_pad=0.4,
+                 grid_kwds=None,
                  params_2_highlight=None,
                  box_color=None,
                  box_fliers=None,
@@ -100,6 +102,10 @@ def __init__(self,
         self.hp_2_hl_idx = np.array([ii for ii, hp in enumerate(self.hp_array)
                                      if hp in self.hp_2_hl]).astype(int)
 
+        self.grid_kwds = self.GRID_KWDS.copy()
+        if grid_kwds is not None:
+            self.grid_kwds.update(grid_kwds)
+
         self.box_color     = box_color
         self.box_fliers    = box_fliers
         self.box_props     = box_props