Forward arguments to violin plot.

libcodonusage/libcodonusage.py

@@ -1089,6 +1089,11 @@ def to_long_form(usage_table, ylabel, others=None):
 
     See https://pandas.pydata.org/docs/user_guide/10min.html#stack
     and https://seaborn.pydata.org/generated/seaborn.violinplot.html
+
+    *y_label* is the column header you want to set for the usage values.
+
+    *others* should be a list of extra information you want to extract
+    from the index (which is expected to be a pandas MultiIndex).
     """
     col_nb_levels = usage_table.columns.nlevels
     row_nb_levels = usage_table.index.nlevels
@@ -1141,7 +1146,9 @@ def format_codon_labels(codons):
         for (x, y, codon) in map(attrgetter("_x", "_y", "_text"), codons)]
 
 
-def violin_usage(usage_table, variable, ylabel, hue="aa", axis=None):
+def violin_usage(
+        usage_table, variable, ylabel,
+        hue="aa", axis=None, **violin_kwargs):
     """
     Plot violin plots of codon usage biases.
 
@@ -1157,15 +1164,20 @@ def violin_usage(usage_table, variable, ylabel, hue="aa", axis=None):
         palette = aa2colour
     else:
         palette = None
-    # if variable == "aa":
-    #     order = list(columns_by_aa.keys())
-    # elif variable == "codon":
-    #     order = [codon for (_, codon) in concat(columns_by_aa.values())]
-    # else:
-    #     raise ValueError("variable can only be 'aa' or 'codon'.\n")
-    sns.violinplot(x=variable, y=ylabel, order=variable2order(variable),
-                   hue=hue, palette=palette, dodge=False,
-                   data=long_form, ax=axis, orient="v", scale="count")
+    if hue in {"aa", "codon"}:
+        dodge = False
+    else:
+        dodge = True
+    kwargs = {
+        "x": variable, "y": ylabel, "order": variable2order(variable),
+        "hue": hue, "palette": palette, "dodge": dodge,
+        "data": long_form, "ax": axis, "orient": "v", "scale": "count"}
+    kwargs.update(violin_kwargs)
+    sns.violinplot(**kwargs)
+    # sns.violinplot(x=variable, y=ylabel, order=variable2order(variable),
+    #                hue=hue, palette=palette, dodge=dodge,
+    #                data=long_form, ax=axis, orient="v", scale="count",
+    #                **violin_kwargs)
     if do_legend:
         plt.legend(bbox_to_anchor=(1.01, 1), borderaxespad=0)
     if variable == "codon":
@@ -1176,7 +1188,9 @@ def violin_usage(usage_table, variable, ylabel, hue="aa", axis=None):
     return axis
 
 
-def violin_usage_vertical(usage_table, variable, ylabel, hue="aa", axis=None):
+def violin_usage_vertical(
+        usage_table, variable, ylabel,
+        hue="aa", axis=None, **violin_kwargs):
     """
     Plot vertically stacked violin plots of codon usage biases.
 
@@ -1189,16 +1203,22 @@ def violin_usage_vertical(usage_table, variable, ylabel, hue="aa", axis=None):
         palette = aa2colour
     else:
         palette = None
-    # if variable == "aa":
-    #     order = list(columns_by_aa.keys())
-    # elif variable == "codon":
-    #     order = [codon for (_, codon) in concat(columns_by_aa.values())]
-    # else:
-    #     raise ValueError("variable can only be 'aa' or 'codon'.\n")
-    sns.violinplot(
-        y=variable, x=ylabel, order=variable2order(variable),
-        hue=hue, palette=palette, dodge=False,
-        data=long_form, ax=axis, orient="h", scale="count")
+    if hue in {"aa", "codon"}:
+        dodge = False
+    else:
+        dodge = True
+    kwargs = {
+        "y": variable, "x": ylabel,
+        "order": variable2order(variable),
+        "hue": hue, "palette": palette, "dodge": dodge,
+        "data": long_form, "ax": axis, "orient": "h", "scale": "count"}
+    kwargs.update(violin_kwargs)
+    sns.violinplot(**kwargs)
+    # sns.violinplot(
+    #     y=variable, x=ylabel, order=variable2order(variable),
+    #     hue=hue, palette=palette, dodge=dodge,
+    #     data=long_form, ax=axis, orient="h", scale="count",
+    #     **violin_kwargs)
     if variable == "codon":
         ticklabels = format_codon_labels(axis.get_yticklabels())
     else: