Added plots

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotHeatmap.R

@@ -21,4 +21,4 @@ dev.off()
 
 png(file = outputArgClustering, width = 1500, height = 1500)
 heatmap.2(heat, trace = 'none', col = col, Colv="Rowv", dendrogram="row",margins = c(10, 10))
-dev.off()
\ No newline at end of file
+dev.off()

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/plotXY.R

+library('gplots')
+library('ggplot2')
+library('reshape2')
+
+args <- commandArgs(TRUE)
+inputArg <- args[1]
+outputArg <- args[2]
+
+print(inputArg)
+print(outputArg)
+
+tsv<-read.table(inputArg, header = 1, sep= '\t', stringsAsFactors = F)
+
+print(inputArg)
+print(outputArg)
+
+data <- melt(tsv)
+#colnames(data) <- c("x", "sample", "value")
+
+data$X <- as.numeric(data$X)
+data <- na.omit(data)
+data <- data[data$value > 0,]
+
+print(inputArg)
+print(outputArg)
+
+print("Starting to plot")
+png(file = outputArg, width = 1500, height = 1500)
+ggplot(data, aes(x=X, y=value, color=variable, group=variable)) + geom_line()
+dev.off()
+print("plot done")

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/tools/VcfStats.scala

@@ -107,6 +107,7 @@ object VcfStats extends ToolCommand {
         writer.println(values.mkString(key + "\t", "\t", ""))
       }
       writer.close()
+      plotXy(file)
     }
   }
 
@@ -149,7 +150,14 @@ object VcfStats extends ToolCommand {
   def plotHeatmap(file: File) {
     val executor = new RScriptExecutor
     executor.addScript(new Resource("plotHeatmap.R", getClass))
-    executor.addArgs(file, file.getAbsolutePath.stripSuffix(".tsv") + ".png", file.getAbsolutePath.stripSuffix(".tsv") + ".clustering.png")
+    executor.addArgs(file, file.getAbsolutePath.stripSuffix(".tsv") + ".heatmap.png", file.getAbsolutePath.stripSuffix(".tsv") + ".heatmap.clustering.png")
+    executor.exec()
+  }
+
+  def plotXy(file: File) {
+    val executor = new RScriptExecutor
+    executor.addScript(new Resource("plotXY.R", getClass))
+    executor.addArgs(file, file.getAbsolutePath.stripSuffix(".tsv") + ".xy.png")
     executor.exec()
   }
 }