Fix violin order. Legend issues.

libcodonusage/__init__.py

 __copyright__ = "Copyright (C) 2022 Blaise Li"
 __licence__ = "GNU GPLv3"
-__version__ = "0.19"
+__version__ = "0.20"
 from .libcodonusage import (
     aa2colour,
     aa_usage,

libcodonusage/libcodonusage.py

@@ -19,7 +19,7 @@ import json
 from operator import itemgetter
 from pathlib import Path
 # python3 -m pip install cytoolz
-from cytoolz import groupby, unique
+from cytoolz import concat, groupby, unique
 # To render mardown in a Jupyter notebook on gitlab
 from IPython.core.display import display, HTML
 # python3 -m pip install markdown
@@ -575,7 +575,7 @@ methionine (M) and tryptophan (W).
         render_md("The following columns contain only NaNs:")
         display(all_nan_cols)
         render_md("This likely resulted from a division by zero.")
-        render_md("These columns will be excluded")
+        render_md("These columns will be excluded.")
     return (
         standardized_usage_biases.drop(columns=all_nan_cols).fillna(0),
         all_nan_cols)
@@ -1118,15 +1118,24 @@ def violin_usage(usage_table, variable, ylabel, hue="aa", axis=None):
     long_form = to_long_form(usage_table, ylabel)
     if axis is None:
         _, axis = plt.subplots(figsize=(18, 6))
+        do_legend = True
+    else:
+        do_legend = False
     if hue == "aa":
         palette = aa2colour
     else:
         palette = None
-    sns.violinplot(x=variable, y=ylabel,
+    if variable == "aa":
+        order = [aa for aa in columns_by_aa.keys()]
+    elif variable == "codon":
+        order = [codon for (_, codon) in concat(columns_by_aa.values())]
+    else:
+        raise ValueError(f"variable can only be 'aa' or 'codon'.\n")
+    sns.violinplot(x=variable, y=ylabel, order=order,
                    hue=hue, palette=palette, dodge=False,
                    data=long_form, ax=axis, orient="v", scale="count")
-    plt.legend(bbox_to_anchor=(1.01, 1),
-               borderaxespad=0)
+    if do_legend:
+        plt.legend(bbox_to_anchor=(1.01, 1), borderaxespad=0)
     axis.set_xticklabels(axis.get_xticklabels(), rotation=90)
     return axis
 
@@ -1144,8 +1153,14 @@ def violin_usage_vertical(usage_table, variable, ylabel, hue="aa", axis=None):
         palette = aa2colour
     else:
         palette = None
+    if variable == "aa":
+        order = [aa for aa in columns_by_aa.keys()]
+    elif variable == "codon":
+        order = [codon for (_, codon) in concat(columns_by_aa.values())]
+    else:
+        raise ValueError(f"variable can only be 'aa' or 'codon'.\n")
     sns.violinplot(
-        y=variable, x=ylabel,
+        y=variable, x=ylabel, order=order,
         hue=hue, palette=palette, dodge=False,
         data=long_form, ax=axis, orient="h", scale="count")
     return axis