# HG changeset patch
# User morinlab
# Date 1488492264 18000
# Node ID f980ebac46b76f9356867012c410994d1fc46b3c
# Parent  1dc706304f98dff479f075f9ef9f2c2b9b594c9b
Uploaded

diff -r 1dc706304f98 -r f980ebac46b7 oncostrip_gistic.R
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/oncostrip_gistic.R	Thu Mar 02 17:04:24 2017 -0500
@@ -0,0 +1,98 @@
+require(maftools);
+library(argparse);
+
+###
+
+parser <- ArgumentParser(description="Create an Oncostrip plot using Maftools");
+
+parser$add_argument(
+    "--input_maf", "-maf",
+    required="True",
+    help="Input Variants in MAF format"
+    );
+
+parser$add_argument(
+    "--gene_list", "-gl",
+    required="True",
+    help="Input gene list with separated by newline"
+    );
+
+
+parser$add_argument(
+   "--output_plot", "-o",
+   required="True",
+   help="Output directory to store gene plots"
+   )
+
+parser$add_argument(
+   "--annotation_file", "-a",
+         help="Annotations for samples"
+	    )
+
+parser$add_argument(
+   "--gistic_all_lesions", "-gal",
+            help="GISTIC output file 1 of 3: all_lesions"
+)
+
+parser$add_argument(
+   "--gistic_amp", "-ga",
+               help="GISTIC output file 2 of 3: amp")
+
+parser$add_argument(
+   "--gistic_del", "-gd",
+               help="GISTIC output file 3 of 3: amp")
+
+parser$add_argument(
+   "--sort_by", "-s",
+   required="True",  
+         help="How to sort the matrix before visualizing, allowed options are 'anno' and 'gene'"
+	)
+
+args <- parser$parse_args();
+
+###
+add_gistic = FALSE
+if(!is.null(args$gistic_all_lesions)){
+	file1 = args$gistic_all_lesions
+	file2 = args$gistic_amp
+	file3 = args$gistic_del
+	add_gistic = TRUE
+}
+
+sort = FALSE
+sort_by_anno = FALSE
+if(args$sort_by == "anno"){
+sort_by_anno=TRUE
+#print(paste("sort_by_anno",sort_by_anno))
+}else if(args$sort_by == "gene"){
+sort=TRUE
+}else{
+
+
+}
+
+###
+
+    
+
+all_genes <- read.table(args$gene_list, stringsAsFactors=FALSE)[,1]
+if(!add_gistic){
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T)
+}else{
+laml = read.maf(maf = args$input_maf, removeSilent = T, useAll = T,gisticAllLesionsFile = file1, gisticAmpGenesFile = file2, gisticDelGenesFile = file3)
+}
+count = 1
+pdf(args$output_plot,width=20,height=20)
+    
+        genes.have = laml@gene.summary[,Hugo_Symbol]
+	    all_genes = all_genes[all_genes %in% genes.have]
+
+
+	    if(is.null(args$annotation_file)){
+	        oncostrip(maf = laml, gene = all_genes, showTumorSampleBarcodes= FALSE, sort=sort)
+		    }else{
+		        df = as.data.frame(read.table(args$annotation_file,sep="\t"))
+			        oncostrip(maf = laml, gene = all_genes, showTumorSampleBarcodes= FALSE, sort=sort,sort_by_anno=sort_by_anno,annotation=df)
+
+    }
+ dev.off()