add SYSUCC label; rearrange dirs

likelet · Jul 28, 2017 · 80c065c · 80c065c
1 parent d5be92d
commit 80c065c
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Showing 4 changed files with 3 additions and 3 deletions.
diff --git a/images/met_VS_tum.png b/images/met_VS_tum.png
diff --git a/forestplot/forest.csv → scriptsWithData/forestplot/forest.csv b/forestplot/forest.csv → scriptsWithData/forestplot/forest.csv
diff --git a/forestplot/forestplot.R → scriptsWithData/forestplot/forestplot.R b/forestplot/forestplot.R → scriptsWithData/forestplot/forestplot.R
diff --git a/scriptsWithData/tumor_vs_met/Tumor vs Met.R b/scriptsWithData/tumor_vs_met/Tumor vs Met.R
@@ -24,8 +24,8 @@ memoSort <- function(M) {
 
 
 #read data 
-met <- fread('scriptsWithData/tumor_vs_met/All_metastasis_filter_mut.maf')
-tum <- fread('scriptsWithData/tumor_vs_met/All_primary_filter_mut.maf')
+met <- fread('scriptsWithData/tumor_vs_met/All_metastasis_filter_mut.maf')[,Tumor_Sample_Barcode := paste0('SYSUCC_', Tumor_Sample_Barcode)]
+tum <- fread('scriptsWithData/tumor_vs_met/All_primary_filter_mut.maf')[,Tumor_Sample_Barcode := paste0('SYSUCC_', Tumor_Sample_Barcode)]
 
 #retain mutations potentially functionally 
 retaind_features=c("frameshift deletion","frameshift insertion","stopgain","nonsynonymous SNV","splicing","stoploss")
@@ -62,7 +62,7 @@ oncomatrix=oncomatrix[,-1]
 oncomatrix=memoSort(oncomatrix!=0)
 
 
-mutations$Samples=factor(mutations$Samples,levels =unique(colnames(oncomatrix)) )
+mutations$Samples=factor(mutations$Samples,levels =unique(colnames(oncomatrix)))
 
 mbar <- ggplot() + 
   geom_col(data = mutations, aes(x = Samples, y = value, fill = Types)) +