Add row or column scaling option to matrixplot

scanpy/plotting/_anndata.py

@@ -1573,7 +1573,9 @@ def dotplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categor
 @doc_params(show_save_ax=doc_show_save_ax, common_plot_args=doc_common_plot_args)
 def matrixplot(adata, var_names, groupby=None, use_raw=None, log=False, num_categories=7,
                figsize=None, dendrogram=False, gene_symbols=None, var_group_positions=None, var_group_labels=None,
-               var_group_rotation=None, layer=None, swap_axes=False, show=None, save=None, **kwds):
+               var_group_rotation=None, layer=None, standard_scale=None, swap_axes=False, show=None,
+               save=None, **kwds):
+
     """\
     Creates a heatmap of the mean expression values per cluster of each var_names
     If groupby is not given, the matrixplot assumes that all data belongs to a single
@@ -1582,6 +1584,9 @@ def matrixplot(adata, var_names, groupby=None, use_raw=None, log=False, num_cate
     Parameters
     ----------
     {common_plot_args}
+    standard_scale : {{'var', 'group'}}, optional (default: None)
+        Whether or not to standardize that dimension, meaning for each variable or group,
+        subtract the minimum and divide each by its maximum.
     {show_save_ax}
     **kwds : keyword arguments
         Are passed to `matplotlib.pyplot.pcolor`.
@@ -1626,6 +1631,17 @@ def matrixplot(adata, var_names, groupby=None, use_raw=None, log=False, num_cate
 
     mean_obs = obs_tidy.groupby(level=0).mean()
 
+    if standard_scale == 'group':
+        mean_obs = mean_obs.sub(mean_obs.min(1), axis=0)
+        mean_obs = mean_obs.div(mean_obs.max(1), axis=0)
+    elif standard_scale == 'var':
+        mean_obs -= mean_obs.min(0)
+        mean_obs /= mean_obs.max(0)
+    elif standard_scale is None:
+        pass
+    else:
+        logg.info('Unknown type for standard_scale, ignored')
+
     if dendrogram:
         dendro_data = _reorder_categories_after_dendrogram(adata, groupby, dendrogram,
                                                            var_names=var_names,

scanpy/tests/test_plotting.py

@@ -81,6 +81,12 @@ def test_matrixplot():
     sc.pl.matrixplot(adata, adata.var_names, 'cell_type', use_raw=False, dendrogram=True, show=False, swap_axes=True)
     save_and_compare_images('master_matrixplot_swap_axes', tolerance=15)
 
+    # test var/group standardization
+    sc.pl.matrixplot(adata, adata.var_names, 'cell_type', use_raw=False, dendrogram=True, show=False, standard_scale='var')
+    save_and_compare_images('master_matrixplot_std_scale_var', tolerance=15)
+    sc.pl.matrixplot(adata, adata.var_names, 'cell_type', use_raw=False, dendrogram=True, show=False, standard_scale='group')
+    save_and_compare_images('master_matrixplot_std_scale_group', tolerance=15)
+
     # test matrixplot numeric column and alternative cmap
     adata.obs['Gata2'] = adata.X[:, 0]
     sc.pl.matrixplot(adata, adata.var_names, 'Gata2', use_raw=False,