From 8ca17aef73cc8d8948a4a59b35fbcbcb545a2407 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Tue, 12 Apr 2022 15:42:24 +0200
Subject: [PATCH] Figure size tweaks, violins by chromosome.
---
libcodonusage/__init__.py | 1 +
libcodonusage/libcodonusage.py | 81 +++++++++++++++++++++++++++-------
2 files changed, 67 insertions(+), 15 deletions(-)
diff --git a/libcodonusage/__init__.py b/libcodonusage/__init__.py
index b2de778..3c99cc9 100644
--- a/libcodonusage/__init__.py
+++ b/libcodonusage/__init__.py
@@ -30,6 +30,7 @@ from .libcodonusage import (
violin_usage,
violin_usage_vertical,
violin_usage_by_clusters,
+ violin_usage_by_clusters_splitby,
violin_with_thresh,
write_cluster_lists,
)
diff --git a/libcodonusage/libcodonusage.py b/libcodonusage/libcodonusage.py
index a4e56a0..ad02e60 100644
--- a/libcodonusage/libcodonusage.py
+++ b/libcodonusage/libcodonusage.py
@@ -1154,9 +1154,17 @@ def violin_usage(
*variable* should be either "codon" or "aa".
"""
+ if hue in {"aa", "codon"}:
+ dodge = False
+ nb_violins = 1
+ else:
+ dodge = True
+ # dodge = True implies there will be one violin
+ # per possible value of *hue*, side by side
+ nb_violins = len(usage_table.index.get_level_values(hue).unique())
long_form = to_long_form(usage_table, ylabel, others=[hue])
if axis is None:
- _, axis = plt.subplots(figsize=(18, 6))
+ _, axis = plt.subplots(figsize=(18 * nb_violins, 6))
do_legend = True
else:
do_legend = False
@@ -1164,10 +1172,6 @@ def violin_usage(
palette = aa2colour
else:
palette = None
- if hue in {"aa", "codon"}:
- dodge = False
- else:
- dodge = True
kwargs = {
"x": variable, "y": ylabel, "order": variable2order(variable),
"hue": hue, "palette": palette, "dodge": dodge,
@@ -1196,17 +1200,21 @@ def violin_usage_vertical(
*variable* should be either "codon" or "aa".
"""
+ if hue in {"aa", "codon"}:
+ dodge = False
+ nb_violins = 1
+ else:
+ dodge = True
+ # dodge = True implies there will be one violin
+ # per possible value of *hue*, side by side
+ nb_violins = len(usage_table.index.get_level_values(hue).unique())
long_form = to_long_form(usage_table, ylabel, others=[hue])
if axis is None:
- _, axis = plt.subplots(figsize=(6, 44))
+ _, axis = plt.subplots(figsize=(6, 44 * nb_violins))
if hue == "aa":
palette = aa2colour
else:
palette = None
- if hue in {"aa", "codon"}:
- dodge = False
- else:
- dodge = True
kwargs = {
"y": variable, "x": ylabel,
"order": variable2order(variable),
@@ -1235,7 +1243,7 @@ def violin_usage_by_clusters(usage_with_clusters, aa, # pylint: disable=C0103
Plot a series of violin plots for each cluster of genes.
The clusters are defined in usage table *usage_with_clusters*
- based on usage biases for the codons codong for amino-acid *aa*.
+ based on usage biases for the codons coding for amino-acid *aa*.
*usage_with_clusters* should have clustering indications as
an index level named according to *cluster_level_template*
@@ -1243,14 +1251,25 @@ def violin_usage_by_clusters(usage_with_clusters, aa, # pylint: disable=C0103
"""
clusters = usage_with_clusters.groupby(
level=cluster_level_template.format(aa=aa))
+ # To adjust figure size
+ if "hue" in violin_kwargs and violin_kwargs["hue"] not in {"aa", "codon"}:
+ # dodge will be set to True in later plotting call.
+ # This implies that there will be one violin
+ # per possible value of *hue*, side by side
+ nb_violins = len(usage_with_clusters.index.get_level_values(
+ violin_kwargs["hue"]).unique())
+ else:
+ nb_violins = 1
if vertical:
- _, axes = plt.subplots(
+ fig, axes = plt.subplots(
ncols=clusters.ngroups,
- figsize=(6 * clusters.ngroups, 44))
+ constrained_layout=True,
+ figsize=(6 * clusters.ngroups, 44 * nb_violins))
else:
- _, axes = plt.subplots(
+ fig, axes = plt.subplots(
nrows=clusters.ngroups,
- figsize=(18, 6 * clusters.ngroups))
+ constrained_layout=True,
+ figsize=(18 * nb_violins, 6 * clusters.ngroups))
for ((cluster, usage_table), axis) in zip(clusters, axes):
kwargs = {"axis": axis}
kwargs.update(violin_kwargs)
@@ -1264,6 +1283,38 @@ def violin_usage_by_clusters(usage_with_clusters, aa, # pylint: disable=C0103
usage_table, "codon",
ylabel_template.format(aa=aa, cluster=cluster),
**kwargs)
+ return fig
+
+
+def violin_usage_by_clusters_splitby(
+ usage_with_clusters, aa, # pylint: disable=C0103
+ ylabel_template,
+ cluster_level_template="cluster_{aa}",
+ vertical=False, by_lvl="chrom",
+ **violin_kwargs):
+ """
+ Plot a series of violin plots for each cluster of genes,
+ splitting the figures according to groups defined by the
+ content of the index level *by_lvl* of *usage_with_clusters*.
+
+ The clusters are defined in usage table *usage_with_clusters*
+ based on usage biases for the codons coding for amino-acid *aa*.
+
+ *usage_with_clusters* should have clustering indications as
+ an index level named according to *cluster_level_template*
+ (default "cluster_{aa}"), where {aa} is to be replaced by *aa*.
+ """
+ classes = sorted(set(
+ usage_with_clusters.index.get_level_values(by_lvl)))
+ idx_level = usage_with_clusters.index.names.index(by_lvl)
+ for clss in classes:
+ fig = violin_usage_by_clusters(
+ usage_with_clusters.loc[
+ (*(slice(None) for _ in range(idx_level)), clss),],
+ aa, ylabel_template + f" for {clss}",
+ cluster_level_template=cluster_level_template,
+ vertical=vertical, **violin_kwargs)
+ fig.suptitle(f"Violin plots for {clss}")
# Based on
--
GitLab