minor edits

elswob · Jul 27, 2015 · fc8bb2f · fc8bb2f
1 parent ead2c06
commit fc8bb2f
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Showing 4 changed files with 12 additions and 5 deletions.
diff --git a/R/pam50_correlation_plot.R b/R/pam50_correlation_plot.R
@@ -40,7 +40,7 @@ multiplot <- function(..., plotlist=NULL, file, cols=1, layout=NULL) {
 #' @param p50 The PAM50 results text file
 #' @param id The ID of the samples to extract
 #' @param name The name to represent the samples
-cor_plot = function(p,id,name){
+cor_plot = function(p,id,name,outDir){
   print(paste0("Generating correlation plots - ",id," - ",name))
   p$X=rownames(p)
   print(head(p))

diff --git a/R/subtypePrediction_distributed.R b/R/subtypePrediction_distributed.R
@@ -42,7 +42,7 @@ pam50_wrapper=function(outDir,inputFile,short){
   # begin analyses
 
   # only need train data for visualizations
-  print(paste0("reading trainFile - ",trainFile))
+  #print(paste0("reading trainFile - ",trainFile))
   x<-readarray(trainFile,hr=2)
   print(summary(x))
   x$xd<-standardize(medianCtr(x$xd))

diff --git a/R/subtype_functions.R b/R/subtype_functions.R
@@ -307,7 +307,7 @@ run_p50=function(pamCC,remove_lc){
   print(head(m)[,0:5])
 
   #inputFile="pam50_median_normalised_10_each.txt"
-  inputFile<-paste0(outDir,"/pam50_median_normalised.txt")
+  inputFile<-paste0(outDir,"/pam50_un-normalised.txt")
 
   ### Run PAM50
   print("Running PAM50")
@@ -383,7 +383,7 @@ run_p50=function(pamCC,remove_lc){
   dev.off()
 
   #plot the correlation coefficients
-  cor_plot(pam.res,".",short)
+  cor_plot(pam.res,".",short,outDir)
 }
 
 ################# SCMGENE #######################

diff --git a/R/subtype_summary.R b/R/subtype_summary.R
@@ -7,12 +7,19 @@ plot_summary=function(m,outDir){
   print(head(m))
   mm<-melt(m,id.vars=1,measure.var=c(5:9))
   mm$value=factor(mm$value,levels=sort(levels(mm$value)))
-  pdf(paste0(outDir,"/subtype_summary.pdf"))
+  pdf(paste0(outDir,"/subtype_summary_pc.pdf"))
   g = ggplot(data = mm, aes(x = sub("_.*","",Sample), fill = value)) + geom_bar(position="fill")
   g = g + labs(title = "Classification counts", y = "Classification Percentage", x = "Sample", fill = "PAM50 Subtype")
   g = g + theme(text = element_text(size=10), axis.text.x = element_text(angle = 90, hjust = 1, size=4))
   print(g)
   dev.off()
+
+  pdf(paste0(outDir,"/subtype_summary_counts.pdf"))
+  g = ggplot(data = mm, aes(x = sub("_.*","",Sample), fill = value)) + geom_bar()
+  g = g + labs(title = "Classification counts", y = "Classification Counts", x = "Sample", fill = "PAM50 Subtype")
+  g = g + theme(text = element_text(size=10), axis.text.x = element_text(angle = 90, hjust = 1, size=4))
+  print(g)
+  dev.off()
 }
 
 #m=read.delim('subtype_summary.tsv')