From 189af8b904f65b821dd3ab246867128b71c69648 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 5 Apr 2022 23:19:51 +0200
Subject: [PATCH] Fix violin order. Legend issues.
---
libcodonusage/__init__.py | 2 +-
libcodonusage/libcodonusage.py | 27 +++++++++++++++++++++------
2 files changed, 22 insertions(+), 7 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index 93cf75e..7ea81e1 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -1,6 +1,6 @@
__copyright__ = "Copyright (C) 2022 Blaise Li"
__licence__ = "GNU GPLv3"
-__version__ = "0.19"
+__version__ = "0.20"
from .libcodonusage import (
aa2colour,
aa_usage,
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index 8f1e0a6..fbf886e 100644
--- a/libcodonusage/libcodonusage.py
+++ b/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
--
GitLab