Adding plots to histograms

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStats.scala

@@ -104,21 +104,14 @@ object BamStats extends ToolCommand {
     val stats = waitOnFutures(processUnmappedReads(bamFile) :: contigsFutures.map(_._2))
 
     stats.flagstat.writeAsTsv(new File(outputDir, "flagstats.tsv"))
-    stats.insertSizeHistogram.writeHistogramToTsv(new File(outputDir, "insertsize.histogram.tsv"))
-    stats.insertSizeHistogram.writeAggregateToTsv(new File(outputDir, "insertsize.stats.tsv"))
-    stats.mappingQualityHistogram.writeHistogramToTsv(new File(outputDir, "mappingQuality.histogram.tsv"))
-    stats.mappingQualityHistogram.writeAggregateToTsv(new File(outputDir, "mappingQualityHistogram.stats.tsv"))
-    stats.clippingHistogram.writeHistogramToTsv(new File(outputDir, "clipping.histogram.tsv"))
-    stats.clippingHistogram.writeAggregateToTsv(new File(outputDir, "clipping.stats.tsv"))
-
-    stats.leftClippingHistogram.writeHistogramToTsv(new File(outputDir, "left_clipping.histogram.tsv"))
-    stats.leftClippingHistogram.writeAggregateToTsv(new File(outputDir, "left_clipping.stats.tsv"))
-    stats.rightClippingHistogram.writeHistogramToTsv(new File(outputDir, "right_clipping.histogram.tsv"))
-    stats.rightClippingHistogram.writeAggregateToTsv(new File(outputDir, "right_clipping.stats.tsv"))
-    stats._3_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "3prime_clipping.histogram.tsv"))
-    stats._3_ClippingHistogram.writeAggregateToTsv(new File(outputDir, "3prime_clipping.stats.tsv"))
-    stats._5_ClippingHistogram.writeHistogramToTsv(new File(outputDir, "5prime_clipping.histogram.tsv"))
-    stats._5_ClippingHistogram.writeAggregateToTsv(new File(outputDir, "5prime_clipping.stats.tsv"))
+    stats.insertSizeHistogram.writeFilesAndPlot(outputDir, "insertsize", "Insertsize", "Reads", "Insertsize distribution")
+    stats.mappingQualityHistogram.writeFilesAndPlot(outputDir, "mappingQuality", "Mapping Quality", "Reads", "Mapping Quality distribution")
+    stats.clippingHistogram.writeFilesAndPlot(outputDir, "clipping", "CLipped bases", "Reads", "Clipping distribution")
+
+    stats.leftClippingHistogram.writeFilesAndPlot(outputDir, "left_clipping", "CLipped bases", "Reads", "Left Clipping distribution")
+    stats.rightClippingHistogram.writeFilesAndPlot(outputDir, "right_clipping", "CLipped bases", "Reads", "Right Clipping distribution")
+    stats._3_ClippingHistogram.writeFilesAndPlot(outputDir, "3prime_clipping", "CLipped bases", "Reads", "3 Prime Clipping distribution")
+    stats._5_ClippingHistogram.writeFilesAndPlot(outputDir, "5prime_clipping", "CLipped bases", "Reads", "5 Prime Clipping distribution")
 
     val statsWriter = new PrintWriter(new File(outputDir, "bamstats.json"))
     val totalStats = stats.toSummaryMap

biopet-tools/src/main/scala/nl/lumc/sasc/biopet/tools/bamstats/Histogram.scala

@@ -14,7 +14,9 @@
  */
 package nl.lumc.sasc.biopet.tools.bamstats
 
-import java.io.{ File, PrintWriter }
+import java.io.{File, PrintWriter}
+
+import nl.lumc.sasc.biopet.utils.rscript.LinePlot
 import nl.lumc.sasc.biopet.utils.sortAnyAny
 
 import scala.collection.mutable
@@ -89,4 +91,16 @@ class Histogram[T](_counts: Map[T, Long] = Map[T, Long]())(implicit ord: Numeric
     writer.close()
   }
 
+  def writeFilesAndPlot(outputDir: File, prefix: String, xlabel: String, ylabel: String, title: String): Unit = {
+    writeHistogramToTsv(new File(outputDir, prefix + ".histogram.tsv"))
+    writeAggregateToTsv(new File(outputDir, prefix + ".stats.tsv"))
+    val plot = new LinePlot(null)
+    plot.input = new File(outputDir, prefix + ".histogram.tsv")
+    plot.output = new File(outputDir, prefix + ".histogram.png")
+    plot.xlabel = Some(xlabel)
+    plot.ylabel = Some(ylabel)
+    plot.title = Some(title)
+    plot.runLocal()
+  }
+
 }

biopet-tools/src/test/scala/nl/lumc/sasc/biopet/tools/bamstats/BamStatsTest.scala

@@ -34,6 +34,15 @@ class BamStatsTest extends TestNGSuite with Matchers {
 
     new File(outputDir, "bamstats.json") should exist
     new File(outputDir, "bamstats.summary.json") should exist
+
+    new File(outputDir, "flagstats.tsv") should exist
+    new File(outputDir, "insertsize.stats.tsv") should exist
+    new File(outputDir, "insertsize.histogram.tsv") should exist
+    new File(outputDir, "mappingQuality.stats.tsv") should exist
+    new File(outputDir, "mappingQuality.histogram.tsv") should exist
+    new File(outputDir, "clipping.stats.tsv") should exist
+    new File(outputDir, "clipping.histogram.tsv") should exist
+
     new File(outputDir, "flagstats") shouldNot exist
     new File(outputDir, "flagstats.summary.json") shouldNot exist
     new File(outputDir, "mapping_quality.tsv") shouldNot exist