possibility to specify axis ticks and the labels used there

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

@@ -42,6 +42,9 @@ class LinePlot(val root: Configurable) extends Rscript {
   var xLog10: Boolean = false
   var yLog10: Boolean = false
 
+  var xLog10AxisTicks: Seq[String] = Seq.empty
+  var xLog10AxisLabels: Seq[String] = Seq.empty
+
   override def cmd = super.cmd ++
     Seq("--input", input.getAbsolutePath) ++
     Seq("--output", output.getAbsolutePath) ++
@@ -53,7 +56,9 @@ class LinePlot(val root: Configurable) extends Rscript {
     title.map(Seq("--title", _)).getOrElse(Seq()) ++
     (if (removeZero) Seq("--removeZero", "true") else Seq()) ++
     (if (xLog10) Seq("--xLog10", "true") else Seq()) ++
-    (if (yLog10) Seq("--yLog10", "true") else Seq())
+    (if (yLog10) Seq("--yLog10", "true") else Seq()) ++
+    (if (xLog10AxisTicks.nonEmpty) xLog10AxisTicks.+:("--xLog10Breaks") else Seq()) ++
+    (if (xLog10AxisTicks.nonEmpty) xLog10AxisLabels.+:("--xLog10Labels") else Seq())
 
 }
 

shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaSvCallingReport.scala

@@ -8,6 +8,7 @@ import nl.lumc.sasc.biopet.utils.summary.Summary
 object ShivaSvCallingReport {
 
   val histogramBinBoundaries: Array[Int] = Array(100, 1000, 10000, 100000, 1000000, 10000000)
+  val histogramPlotTicks: Array[Int] = Array(100, 1000, 10000, 100000, 1000000, 10000000, 100000000)
   val histogramText: List[String] = List("<=100bp", "0.1-1kb", "1-10kb", "10-100kb", "0.1-1Mb", "1-10Mb", ">10Mb")
 
   def parseSummaryForSvCounts(summary: Summary): Map[String, Map[String, Array[Any]]] = {
@@ -60,15 +61,11 @@ object ShivaSvCallingReport {
     sampleNames.foreach(sampleName => tsvWriter.print("\t" + sampleName))
     tsvWriter.println()
 
-    for (i <- histogramBinBoundaries.indices) {
-      tsvWriter.print(histogramBinBoundaries(i))
+    for (i <- histogramPlotTicks.indices) {
+      tsvWriter.print(histogramPlotTicks(i))
       sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get(i)))
       tsvWriter.println()
     }
-    val i = histogramBinBoundaries.length
-    tsvWriter.print(histogramBinBoundaries(i - 1) * 10)
-    sampleNames.foreach(sampleName => tsvWriter.print("\t" + counts.get(sampleName).get(i)))
-    tsvWriter.println()
 
     tsvWriter.close()
   }
@@ -87,6 +84,8 @@ object ShivaSvCallingReport {
       plot.llabel = Some("Sample")
       plot.xLog10 = true
       plot.yLog10 = true
+      plot.xLog10AxisTicks = histogramPlotTicks.collect({ case x => x.toString() })
+      plot.xLog10AxisLabels = histogramText
       plot.runLocal()
     }