Added extension for stacked bar plot

public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/tools/stackedBar.R → public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/stackedBar.R

@@ -25,7 +25,9 @@ DF1 <- melt(DF, id.var="Rank")
 
 ggplot(DF1, aes(x = Rank, y = value, fill = variable)) + 
   xlab(xlab) +
-  ylab(arguments$ylabel) + guides(fill=guide_legend(title=arguments$llabel)) +
-  geom_bar(stat = "identity")
+  ylab(arguments$ylabel) + 
+  guides(fill=guide_legend(title=arguments$llabel)) +
+  theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+  geom_bar(stat = "identity", width=0.75)
 
 dev.off()

public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/StackedBarPlot.scala

+package nl.lumc.sasc.biopet.extensions.rscript
+
+import java.io.File
+
+import nl.lumc.sasc.biopet.core.config.Configurable
+import nl.lumc.sasc.biopet.extensions.RscriptCommandLineFunction
+import org.broadinstitute.gatk.utils.commandline.{Output, Input}
+
+/**
+ * Created by pjvan_thof on 4/29/15.
+ */
+class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction {
+  protected var script: File = config("script", default = "stackedBar.R")
+
+  @Input
+  var input: File = _
+
+  @Output
+  var output: File = _
+
+  var width: Option[Int] = config("width")
+  var height: Option[Int] = config("height")
+  var xlabel: Option[String] = config("xlabel")
+  var ylabel: Option[String] = config("ylabel")
+  var llabel: Option[String] = config("llabel")
+
+  override def cmdLine: String = super.cmdLine +
+    required("--input", input) +
+    required("--output", output) +
+    optional("--width", width) +
+    optional("--height", height) +
+    optional("--xlabel", xlabel) +
+    required("--ylabel", ylabel) +
+    optional("--llabel", llabel)
+}