Remove legends on plot when there to many samples

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

@@ -208,6 +208,7 @@ object BammetricsReport extends ReportBuilder {
       xlabel = xlabel,
       ylabel = ylabel,
       title = title,
+      hideLegend = results.size > 40,
       removeZero = removeZero).runLocal()
   }
 

biopet-utils/src/main/resources/nl/lumc/sasc/biopet/utils/rscript/plotXY.R

@@ -11,6 +11,7 @@ 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')
+parser$add_argument('--hideLegend', dest='hideLegend', type='character', default="false")
 parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
 
 arguments <- parser$parse_args()
@@ -21,6 +22,8 @@ DF <- read.table(arguments$input, header=TRUE)
 
 if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
 
+if (is.null(arguments$hideLegend) || arguments$hideLegend == "false") legendPosition <- "right" else legendPosition <- "none"
+
 colnames(DF)[1] <- "Rank"
 
 DF1 <- melt(DF, id.var="Rank")
@@ -35,6 +38,7 @@ ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
   theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
   ggtitle(arguments$title) +
   theme_bw() +
+  theme(legend.position = legendPosition) +
   geom_line()
 
 dev.off()

biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/rscript/LinePlot.scala

@@ -36,6 +36,7 @@ class LinePlot(val parent: Configurable) extends Rscript {
   var ylabel: Option[String] = config("ylabel")
   var llabel: Option[String] = config("llabel")
   var title: Option[String] = config("title")
+  var hideLegend: Boolean = config("hide_legend", default = false)
   var removeZero: Boolean = config("removeZero", default = false)
 
   override def cmd = super.cmd ++
@@ -47,6 +48,7 @@ class LinePlot(val parent: Configurable) extends Rscript {
     ylabel.map(Seq("--ylabel", _)).getOrElse(Seq()) ++
     llabel.map(Seq("--llabel", _)).getOrElse(Seq()) ++
     title.map(Seq("--title", _)).getOrElse(Seq()) ++
+    (if (hideLegend) Seq("--hideLegend", "true") else Seq()) ++
     (if (removeZero) Seq("--removeZero", "true") else Seq())
 }
 
@@ -57,6 +59,7 @@ object LinePlot {
             xlabel: Option[String] = None,
             ylabel: Option[String] = None,
             width: Int = 1200,
+            hideLegend: Boolean = false,
             removeZero: Boolean = false,
             title: Option[String] = None): LinePlot = {
     val plot = new LinePlot(root)
@@ -65,6 +68,7 @@ object LinePlot {
     plot.xlabel = xlabel
     plot.ylabel = ylabel
     plot.width = Some(width)
+    plot.hideLegend = hideLegend
     plot.removeZero = removeZero
     plot.title = title
     plot