initial upload

src/R/upset.R

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+#!/usr/bin/env Rscript
+#
+# Plot VCFCompare.py UpSet Plots
+#
+# This script requires UpSetR and argepase packages.
+# To install the packages, run the following commandc in R:
+#
+#   install.packages("UpSetR")
+#   install.packages("argeparse")
+#
+# Usage:
+#
+# This script runs on a set of VCFCompare.py results. Result n will have been run
+# with VCFCompare.py -o prefix_n.
+#
+# run Rscript upsetr.Rscript [-i] file.csv -o output_prefix
+
+library(UpSetR)
+library(argparse)
+
+#Command line
+parser <- ArgumentParser()
+parser <- ArgumentParser(description='This is an extension of VCFCompare. Use this script to plot upset plots.')
+parser$add_argument('-i', help='This is the input CSV file generated using VCFCompare.py')
+parser$add_argument('-o', help='Output prefix filename for upset plots')
+args <- parser$parse_args()
+input <- args$i
+output_prefix <- args$o
+
+#Error handling
+if (!file.exists(input)){
+sprintf("File %s does not exist.", input)
+stop(input, " does not exist")
+}
+
+file = read.csv(input)
+
+### 1.SNPs ###
+truthSNVunique <- file$FN[1]
+querySNVunique <- file$FP[1]
+SNVintersect <- file$TP[1]
+expressionSNV <- c(Truth = truthSNVunique, Query = querySNVunique,
+                        `Truth&Query` = SNVintersect)
+
+pdf(paste(output_prefix, "SNV", "pdf", sep="."))
+upset(fromExpression(expressionSNV),
+      main.bar.color = "black",
+      sets.bar.color = "black",
+      matrix.color = "black",
+      point.size=5,
+      order.by = "freq")
+dev.off()
+
+### 2.INDELs ###
+truthINDELunique <- file$FN[2]
+queryINDELunique <- file$FP[2]
+INDELintersect <- file$TP[2]
+expressionINDEL <- c(Truth = truthINDELunique, Query = queryINDELunique,
+                   `Truth&Query` = INDELintersect)
+
+pdf(paste(output_prefix, "INDEL", "pdf", sep="."))
+upset(fromExpression(expressionINDEL),
+      main.bar.color = "black",
+      sets.bar.color = "black",
+      matrix.color = "black",
+      point.size=5,
+      order.by = "freq")
+dev.off()