Merge pull request #52 from sbslee/1.16.0-dev

1.16.0 dev

CHANGELOG.rst

@@ -1,6 +1,12 @@
 Changelog
 *********
 
+1.16.0 (2022-12-27)
+-------------------
+
+* Add new argument ``palette`` to :meth:`taxa_abundance_box_plot` method.
+* :issue:`51`: Fix bug in :meth:`clustermap` method where color labels disappeared when ``flip=True``.
+
 1.15.0 (2022-08-23)
 -------------------
 

dokdo/api/clustermap.py

@@ -337,9 +337,13 @@ def clustermap(
 
     .. image:: images/clustermap-3.png
 
-    We can add an additional grouping variable ``subject``. Note that
-    ``xticklabels`` and ``yticklabels`` are extra keyword arguments that
-    are passed to :meth:`seaborn.clustermap`.
+    We can add an additional grouping variable ``subject``. This may require
+    you to use ``bbox_inches='tight'`` option in the :meth:`plt.savefig`
+    method when saving the figure as a file (e.g. PNG) because otherwise
+    there could be weird issues with the legends (because there are now two
+    legends instead of just one). Additionally, note that ``xticklabels``
+    and ``yticklabels`` are extra keyword arguments that are passed to
+    :meth:`seaborn.clustermap`.
 
     .. code:: python3
 
@@ -350,6 +354,7 @@ def clustermap(
                          hue2='subject',
                          xticklabels=False,
                          yticklabels=False)
+        plt.savefig('out.png', bbox_inches='tight')
 
     .. image:: images/clustermap-4.png
 
@@ -410,11 +415,13 @@ def clustermap(
     # Flip the axes.
     if flip:
         df = df.T
-
-    # Draw the heatmap.
-    g = sns.clustermap(df, method=method, metric=metric, figsize=figsize,
-                       row_cluster=row_cluster, col_cluster=col_cluster,
-                       row_colors=row_colors, **kwargs)
+        g = sns.clustermap(df, method=method, metric=metric, figsize=figsize,
+                           row_cluster=row_cluster, col_cluster=col_cluster,
+                           col_colors=row_colors, **kwargs)
+    else:
+        g = sns.clustermap(df, method=method, metric=metric, figsize=figsize,
+                           row_cluster=row_cluster, col_cluster=col_cluster,
+                           row_colors=row_colors, **kwargs)
 
     # If the hue argument(s) are used, add the legend(s).
     if hue1 is not None:

dokdo/api/taxa_abundance.py

@@ -649,7 +649,7 @@ def taxa_abundance_box_plot(
     sample_names=None, csv_file=None, pseudocount=False,
     taxa_names=None, pretty_taxa=False, show_means=False,
     meanprops=None, show_others=True, sort_by_mean=True,
-    add_datapoints=False, jitter=1, alpha=None, size=5,
+    add_datapoints=False, jitter=1, alpha=None, size=5, palette=None,
     ax=None, figsize=None,
 ):
     """
@@ -729,6 +729,8 @@ def taxa_abundance_box_plot(
     size : float, default: 5.0
         Ignored when ``add_datapoints=False``. Radius of the markers, in
         points.
+    palette : palette name, list, or dict
+        Box colors.
     ax : matplotlib.axes.Axes, optional
         Axes object to draw the plot onto, otherwise uses the current Axes.
     figsize : tuple, optional
@@ -929,7 +931,7 @@ def taxa_abundance_box_plot(
 
     sns.boxplot(
         x='variable', y='value', hue=hue, hue_order=hue_order, data=df2,
-        ax=ax, **d
+        ax=ax, palette=palette, **d
     )
 
     if add_datapoints:

dokdo/version.py

@@ -1 +1 @@
-__version__ = '1.15.0'
+__version__ = '1.16.0'