From 18a4466259d89cfe835ae32f20a72e8b66ad7b2a Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 19 Aug 2015 15:52:16 +0200
Subject: [PATCH] Added a scatter plot
---
.../biopet/extensions/rscript/plotScatter.R | 40 +++++++++++++
.../extensions/rscript/ScatterPlot.scala | 56 +++++++++++++++++++
2 files changed, 96 insertions(+)
create mode 100644 public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
create mode 100644 public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
diff --git a/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
new file mode 100644
index 000000000..a1959a262
--- /dev/null
+++ b/public/biopet-framework/src/main/resources/nl/lumc/sasc/biopet/extensions/rscript/plotScatter.R
@@ -0,0 +1,40 @@
+library(reshape2)
+library(ggplot2)
+library(argparse)
+
+parser <- ArgumentParser(description='Process some integers')
+parser$add_argument('--input', dest='input', type='character', help='Input tsv file', required=TRUE)
+parser$add_argument('--output', dest='output', type='character', help='Output png file', required=TRUE)
+parser$add_argument('--width', dest='width', type='integer', default = 500)
+parser$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')
+parser$add_argument('--removeZero', dest='removeZero', type='character', default="false")
+
+arguments <- parser$parse_args()
+
+png(filename = arguments$output, width = arguments$width, height = arguments$height)
+
+DF <- read.table(arguments$input, header=TRUE)
+
+if (is.null(arguments$xlabel)) xlab <- colnames(DF)[1] else xlab <- arguments$xlabel
+
+colnames(DF)[1] <- "Rank"
+
+DF1 <- melt(DF, id.var="Rank")
+
+if (arguments$removeZero == "true") DF1 <- DF1[DF1$value > 0, ]
+if (arguments$removeZero == "true") print("Removed 0 values")
+
+ggplot(DF1, aes(x = Rank, y = value, group = variable, color = variable)) +
+ xlab(xlab) +
+ ylab(arguments$ylabel) +
+ guides(fill=guide_legend(title=arguments$llabel)) +
+ theme(axis.text.x = element_text(angle = 90, hjust = 1, size = 8)) +
+ ggtitle(arguments$title) +
+ theme_bw() +
+ geom_point()
+
+dev.off()
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
new file mode 100644
index 000000000..e03ce0b4b
--- /dev/null
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/rscript/ScatterPlot.scala
@@ -0,0 +1,56 @@
+/**
+ * Biopet is built on top of GATK Queue for building bioinformatic
+ * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
+ * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
+ * should also be able to execute Biopet tools and pipelines.
+ *
+ * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
+ *
+ * Contact us at: sasc@lumc.nl
+ *
+ * A dual licensing mode is applied. The source code within this project that are
+ * not part of GATK Queue is freely available for non-commercial use under an AGPL
+ * license; For commercial users or users who do not want to follow the AGPL
+ * license, please contact us to obtain a separate license.
+ */
+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.{Input, Output}
+
+/**
+ * Extension for en general line plot with R
+ *
+ * Created by pjvan_thof on 4/29/15.
+ */
+class ScatterPlot(val root: Configurable) extends RscriptCommandLineFunction {
+ protected var script: File = config("script", default = "plotScatter.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")
+ var title: Option[String] = config("title")
+ var removeZero: Boolean = config("removeZero", default = false)
+
+ 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) +
+ optional("--title", title) +
+ optional("--removeZero", removeZero)
+}
--
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