Add title to some plots

public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala

@@ -84,6 +84,7 @@ object BammetricsReport extends ReportBuilder {
     plot.output = pngFile
     plot.ylabel = Some("Reads")
     plot.width = Some(750)
+    plot.title = Some("Aligned reads")
     plot.runLocal()
   }
 

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

@@ -10,6 +10,7 @@ parser$add_argument('--height', dest='height', type='integer', default = 500)
 parser$add_argument('--xlabel', dest='xlabel', type='character')
 parser$add_argument('--ylabel', dest='ylabel', type='character', required=TRUE)
 parser$add_argument('--llabel', dest='llabel', type='character')
+parser$add_argument('--title', dest='title', type='character')
 
 arguments <- parser$parse_args()
 
@@ -28,6 +29,7 @@ ggplot(DF1, aes(x = Rank, y = value, fill = variable)) +
   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=1)
+  geom_bar(stat = "identity", width=1) +
+  ggtitle(arguments$title)
 
 dev.off()

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

@@ -23,6 +23,7 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
   var xlabel: Option[String] = config("xlabel")
   var ylabel: Option[String] = config("ylabel")
   var llabel: Option[String] = config("llabel")
+  var title: Option[String] = config("title")
 
   override def cmdLine: String = super.cmdLine +
     required("--input", input) +
@@ -31,5 +32,6 @@ class StackedBarPlot(val root: Configurable) extends RscriptCommandLineFunction
     optional("--height", height) +
     optional("--xlabel", xlabel) +
     required("--ylabel", ylabel) +
-    optional("--llabel", llabel)
+    optional("--llabel", llabel) +
+    optional("--title", title)
 }

public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala

@@ -88,6 +88,7 @@ object FlexiprepReport extends ReportBuilder {
     plot.output = pngFile
     plot.ylabel = Some("Reads")
     plot.width = Some(750)
+    plot.title = Some("QC summary on " + read + " reads")
     plot.runLocal()
   }
 
@@ -128,6 +129,7 @@ object FlexiprepReport extends ReportBuilder {
     plot.output = pngFile
     plot.ylabel = Some("Bases")
     plot.width = Some(750)
+    plot.title = Some("QC summary on " + read + " bases")
     plot.runLocal()
   }
 }