From 0458f11d58e98c5ab25d5449fe52422ba0404c3c Mon Sep 17 00:00:00 2001
From: Fontrodona Nicolas <nicolas.fontrodona@ens-lyon.fr>
Date: Wed, 27 Jan 2021 16:40:33 +0100
Subject: [PATCH] src/gc_content/gc_content.py: change graphic style of the
figure
---
src/gc_content/gc_content.py | 9 ++++++++-
1 file changed, 8 insertions(+), 1 deletion(-)
diff --git a/src/gc_content/gc_content.py b/src/gc_content/gc_content.py
index b34e871..c517c44 100644
--- a/src/gc_content/gc_content.py
+++ b/src/gc_content/gc_content.py
@@ -19,6 +19,7 @@ from pathlib import Path
import seaborn as sns
from .gc_stats import make_stat
from .stat_annot import add_stat_annotation
+import matplotlib.font_manager
def get_gc_content(bed_line: List[Any], dic_seq: Fasta) -> float:
@@ -139,7 +140,11 @@ def make_gc_barplot(df: pd.DataFrame, outfile: Path, environment: int,
:param region_names: The name of the regions analysed
:param ft_name: The name of the feature analyzed
"""
- sns.set(context="poster")
+ font_files = matplotlib.font_manager.findSystemFonts(fontpaths=None,
+ fontext='ttf')
+ font_list = matplotlib.font_manager.createFontList(font_files)
+ matplotlib.font_manager.fontManager.ttflist.extend(font_list)
+ sns.set(context="poster", style="white", font="Arial", font_scale=1.4)
rgn = ", ".join(region_names[:-1]) + " and " + region_names[-1]
title = f"GC content of {rgn} {ft_name}"
p_vals = make_stat(df)
@@ -164,6 +169,7 @@ def make_gc_barplot(df: pd.DataFrame, outfile: Path, environment: int,
g.set_ylabels("GC content")
g.set_xlabels("")
g.fig.subplots_adjust(top=0.9)
+ g.ax.tick_params(left=True, bottom=True)
g.fig.suptitle(title + " and their surrounding regions "
f"of {environment} nucleotides")
g.savefig(outfile)
@@ -187,6 +193,7 @@ def create_barplot(beds: List[Path], bed_names: List[str],
df = build_gc_dataframe(bed_content, dic_seq, environment, ft_name)
outfile = ConfigGC.output / \
f"gc_content_{'-'.join(bed_names)}_env_{environment}_nt.pdf"
+ df.to_csv(str(outfile).replace(".pdf", ".txt"), index=False, sep="\t")
outfile.parent.mkdir(exist_ok=True, parents=True)
make_gc_barplot(df, outfile, environment, bed_names, ft_name)
--
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