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AllenInstitute · Sep 1, 2023 · f45eb84 · f45eb84
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Showing 8 changed files with 3,084 additions and 1,675 deletions.
diff --git a/notebooks/l1_cross_species.ipynb b/notebooks/l1_cross_species.ipynb
diff --git a/notebooks/l1_depth_revisions.ipynb b/notebooks/l1_depth_revisions.ipynb
diff --git a/notebooks/l1_dprime.ipynb b/notebooks/l1_dprime.ipynb
diff --git a/notebooks/l1_rosehip.ipynb b/notebooks/l1_rosehip.ipynb
diff --git a/notebooks/l1_subclass_distinctness.ipynb b/notebooks/l1_subclass_distinctness.ipynb
diff --git a/notebooks/l1_tnfaip.ipynb b/notebooks/l1_tnfaip.ipynb
diff --git a/patchseq_utils/analysis.py b/patchseq_utils/analysis.py
@@ -145,11 +145,11 @@ def plot_box_cluster_feature(data, y, x='cluster', x_fine=None, label=None, ax=N
                     drop_box=False,
                     test='mannwhitney', pairs='all', cutoff=0.05, fdr_method='fdr_bh', test_label=None,
                     invert_y=False, label_yaxis=False, pad_title=0, title_loc='right',
-                    label_counts=True, label_color=False, size=3, highlight=None, 
+                    label_counts=True, label_color=False, size=4, highlight=None, 
                     label_align='right',
                     legend=None, **kwargs
                     ):
-    data = remove_unused_categories(data.dropna(subset=[x,y]).copy())
+    # data = remove_unused_categories(data.dropna(subset=[x,y]).copy())
     if not hasattr(data[x], 'cat'):
         # make column ordered categorical
         data[x] = data[x].astype('category')
@@ -559,7 +559,7 @@ def run_twosamp(df, features, variable, fdr_method='fdr_bh', sort_by='pval_mw'):
         subsets = [group[feature] for val, group in grouped]
         assert len(subsets) == 2
         nums = grouped.size().values
-        u, pval_mw = stats.mannwhitneyu(subsets[0], subsets[1])
+        u, pval_mw = stats.mannwhitneyu(subsets[0], subsets[1], method='exact')
         roc_auc = u/(nums[0]*nums[1])
         roc_auc = roc_auc if roc_auc > 0.5 else 1 - roc_auc
         mw_r = 2*roc_auc - 1

diff --git a/patchseq_utils/plotting.py b/patchseq_utils/plotting.py
@@ -84,10 +84,11 @@ def plot_subclass_focus(df, y, x, ax, subclasses, label=None, cluster="t-type",
                     palette_fine=palette_fine, palette=palette)
         args.update(**kwargs)
         utils.plot_box_cluster_feature(data, y, x, x_fine=cluster, ax=ax, pairs=None, **args)
+    else:
+        utils.outline_boxplot(ax)
     if pairs is not None:
         utils.plot_test_bars(df, y, x, test=test, group_vals=None, pairs=pairs, fdr_method=fdr_method,
                     ax=ax, cutoff=cutoff, label=None)
-    utils.outline_boxplot(ax)
     ax.set_xlabel(None)
 
 def plot_scatter(*args, legend=False, figsize=(8,8), **kwargs):