From f569056ed33a70395d3e8a41b3a32fe14a0333d3 Mon Sep 17 00:00:00 2001
From: Shaman Narayanasamy <shaman.narayanasamy@uni.lu>
Date: Sat, 25 Jul 2015 14:06:23 +0200
Subject: [PATCH] Change bandwidth for plotting method
---
src/IMP_visualize_MGMT.R | 6 +++---
1 file changed, 3 insertions(+), 3 deletions(-)
diff --git a/src/IMP_visualize_MGMT.R b/src/IMP_visualize_MGMT.R
index 0c76c86..9c61682 100755
--- a/src/IMP_visualize_MGMT.R
+++ b/src/IMP_visualize_MGMT.R
@@ -775,7 +775,7 @@ dev.off()
var1 <-log10(c(all.dat$MG_var,all.dat$MT_var))
var1[is.infinite(var1)]=NA
var2 <- c(rep("MG",nrow(all.dat)),rep("MT",nrow(all.dat)))
-variant_count<-data.frame(var1,var2)
+variant_count <- data.frame(var1,var2)
print("Generating variant count plots")
png(name_plot("IMP-var_count.png") ,width=700, height=700)
@@ -783,7 +783,7 @@ png(name_plot("IMP-var_count.png") ,width=700, height=700)
par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
beanplot(var1 ~ var2, data= variant_count, side = "both",log="auto",
what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
-main="Variant count", ylab=expression(log[10]*~count))
+main="Variant count", ylab=expression(log[10]*~count), bw="nrd")
legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
dev.off()
@@ -799,7 +799,7 @@ png(name_plot("IMP-var_density.png") ,width=700, height=700)
par(lend = 1, mai = c(0.8, 0.8, 0.5, 0.5))
beanplot(var1 ~ var2, data= variant_density, side = "both",log="auto",
what=c(1,1,1,0), border = NA, col = list("blue", c("red", "white")),
-main="Variant density", ylab="count / RPKM")
+main="Variant density", ylab="count / RPKM", bw="nrd")
legend("bottomleft", fill =c("blue", "red"), legend = c("MG", "MT"))
dev.off()
--
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