From b81d3288aab9b66620c4b9f6cc2b0c140bd56828 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Flor=C3=A9al=20Cabanettes?= <floreal.cabanettes@inra.fr>
Date: Thu, 20 Apr 2017 14:31:20 +0200
Subject: [PATCH] Add colors to boxplots
---
build_R_figures.py | 21 +++++++++++++++------
1 file changed, 15 insertions(+), 6 deletions(-)
diff --git a/build_R_figures.py b/build_R_figures.py
index a14f937..95ce17c 100755
--- a/build_R_figures.py
+++ b/build_R_figures.py
@@ -38,6 +38,8 @@ with open(rscript_name, "w") as rscript:
columns = []
columns_goods = []
columns_bads = []
+ rscript.write("colors <- colorRampPalette(c(\"#ff0000\", \"#e6e600\", \"#00ff00\"));\n"
+ "colors <- colors(101);\n")
for indiv in range(1, args.nb_inds+1):
columns.append("gt_qual[,\"{0}__INDIV_{1}\"]".format(tool, indiv))
columns_goods.append("gt_qual_goods[,\"{0}__INDIV_{1}\"]".format(tool, indiv))
@@ -54,21 +56,28 @@ with open(rscript_name, "w") as rscript:
"\t}}\n" +
"}}\n").format(tool, indiv))
+ colors = ["colors[round(mean(" + x + ", na.rm = T))+1]" for x in columns]
+ colors_goods = ["colors[round(mean(" + x + ", na.rm = T))+1]" for x in columns_goods]
+ colors_bads = ["colors[round(mean(" + x + ", na.rm = T))+1]" for x in columns_bads]
+
# All
rscript.write("pdf(\"gt_quality_" + tool + ".pdf\", width=9, height=3);\n")
rscript.write("par(mfrow=c(1,3));\n")
- rscript.write("boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100));\n".
- format(", ".join(columns), tool.title() + " [ALL]"))
+ rscript.write(
+ "boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100), border=c({2}));\n".
+ format(", ".join(columns), tool.title() + " [ALL]", ",".join(colors)))
rscript.write("axis(side=1, seq(1,{0}));\n".format(args.nb_inds))
# Goods
- rscript.write("boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100));\n".
- format(", ".join(columns_goods), tool.title() + " [GOODS]"))
+ rscript.write(
+ "boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100), border=c({2}));\n".
+ format(", ".join(columns_goods), tool.title() + " [GOODS]", ",".join(colors_goods)))
rscript.write("axis(side=1, seq(1,{0}));\n".format(args.nb_inds))
# Bads
- rscript.write("boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100));\n".
- format(", ".join(columns_bads), tool.title() + " [BADS]"))
+ rscript.write(
+ "boxplot({0}, main=\"{1}\", xlab=\"individuals\", ylab=\"quality (%)\", ylim=c(0,100), border=c({2}));\n".
+ format(", ".join(columns_bads), tool.title() + " [BADS]", ",".join(colors_bads)))
rscript.write("axis(side=1, seq(1,{0}));\n".format(args.nb_inds))
sv_file_io = open(svs_file, "r")
--
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