changeset 10:ab0d51ba4a7b draft default tip

Deleted selected files

--- a/oncostrip_gistic.R	Thu Mar 02 17:04:59 2017 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,98 +0,0 @@
-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$output_plot,width=20,height=20)
-    
-        genes.have = [e-mail][,Hugo_Symbol]
-	    all_genes = all_genes[all_genes %in% genes.have]
-
-
-	    if(is.null(args$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()