From 74753080de9c4a801619f654fbfbcf3906b9c565 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Wed, 15 May 2019 18:42:17 +0200
Subject: [PATCH] Plot gene lists without selection_label set.
Also switched to read_csv to remove warnings.
The latex processing fails when no X server is available, it seems that
xcolor package is not loaded.
---
plot_lfclfc_scatter.py | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/plot_lfclfc_scatter.py b/plot_lfclfc_scatter.py
index a561786..9478e63 100755
--- a/plot_lfclfc_scatter.py
+++ b/plot_lfclfc_scatter.py
@@ -97,11 +97,11 @@ class Scatterplot:
else:
x_usecols = ["gene", x_column, *extra_cols].__contains__
y_usecols = ["gene", y_column, *extra_cols].__contains__
- x_data = pd.read_table(
- x_input_file, index_col="gene", usecols=x_usecols).rename(
+ x_data = pd.read_csv(
+ x_input_file, sep="\t", index_col="gene", usecols=x_usecols).rename(
columns={x_column: "x"})
- y_data = pd.read_table(
- y_input_file, index_col="gene", usecols=y_usecols).rename(
+ y_data = pd.read_csv(
+ y_input_file, sep="\t", index_col="gene", usecols=y_usecols).rename(
columns={y_column: "y"})
# Just some experiments
# from cytoolz import merge_with
@@ -445,7 +445,7 @@ def main():
"%s.log" % args.plot_name)
with open(out_log, "w") as log_file:
print(" \\\n\t".join(sys.argv), file=log_file)
- if gene_list and args.selection_label:
+ if gene_list:
plot_data.data.assign(hightlighted=plot_data.data.apply(
# apply takes a function of row
# get the row name
@@ -453,7 +453,8 @@ def main():
compose(curry(contains)(gene_list), attrgetter("name")),
axis=1)).to_csv(
out_table, sep="\t")
- list_name = args.selection_label
+ if args.selection_label:
+ list_name = args.selection_label
# if args.gene_list:
# if args.selection_label:
# list_name = args.selection_label
--
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