# HG changeset patch
# User davidvanzessen
# Date 1433237638 14400
# Node ID dde5ec84754940471c5338f0c43933a2c2acd30a
# Parent  ce8bd23d033537c716a5ef66b9a4b47b14c0748a
Uploaded

diff -r ce8bd23d0335 -r dde5ec847549 RScript.r
--- a/RScript.r	Tue Jun 02 05:26:52 2015 -0400
+++ b/RScript.r	Tue Jun 02 05:33:58 2015 -0400
@@ -289,7 +289,7 @@
 cat("</table></html>", file=logfile, append=T)
 
 scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
-p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
+p = ggplot(single_patients, aes(Rearrangement, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
 p = p + geom_point(aes(colour=type), position="jitter")
 p = p + xlab("In one or both samples") + ylab("Reads")
 p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the reads of the patients with a single sample")
@@ -297,7 +297,7 @@
 print(p)
 dev.off()
 
-p = ggplot(single_patients, aes(Rearrangement, Frequency))
+p = ggplot(single_patients, aes(Rearrangement, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
 p = p + geom_point(aes(colour=type), position="jitter")
 p = p + xlab("In one or both samples") + ylab("Frequency")
 p = p + facet_grid(.~Patient) + ggtitle("Scatterplot of the frequency of the patients with a single sample")
@@ -448,9 +448,9 @@
       if(nrow(scatterplot_locus_data) != 0){
         if(on == "normalized_read_count"){
 					scales = 10^(0:6) #(0:ceiling(log10(max(scatterplot_locus_data$normalized_read_count))))
-          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales)
+          p = ggplot(scatterplot_locus_data, aes(type, normalized_read_count)) + scale_y_log10(breaks=scales,labels=scales) + expand_limits(y=c(0,1000000))
         } else {
-          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) 
+          p = ggplot(scatterplot_locus_data, aes(type, Frequency)) + scale_y_continuous(limits = c(0, 100)) + expand_limits(y=c(0,100))
         }
         p = p + geom_point(aes(colour=type), position="jitter")
         p = p + xlab("In one or in multiple samples") + ylab(onShort) + ggtitle(paste(label1, label2, label3, onShort, product[iter, titleIndex]))