TCGA Chart

Data obtained from Facilitating Exploratory Data Visualization: Application to TCGA Genomic Data.



Color Themes


{
   "boxplotWhiskersType" : "single",
   "colorBy" : "dataset",
   "colorScheme" : "JCO",
   "graphOrientation" : "vertical",
   "graphType" : "Boxplot",
   "groupingFactors" : ["dataset"],
   "histogramBins" : "150",
   "layoutTopology" : "1X3",
   "legendColumns" : "3",
   "legendPosition" : "top",
   "legendScaleFontFactor" : 1.5,
   "segregateVariablesBy" : ["variable"],
   "showViolinBoxplot" : "true",
   "smpLabelRotate" : "90",
   "toolbarType" : "over",
   "useOpenShapes" : "true"
}
library(canvasXpress)
y=read.table("https://www.canvasxpress.org/data/cX-exprtcga-dat.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
x=read.table("https://www.canvasxpress.org/data/cX-exprtcga-smp.txt", header=TRUE, sep="\t", quote="", row.names=1, fill=TRUE, check.names=FALSE, stringsAsFactors=FALSE)
canvasXpress(
  data=y,
  smpAnnot=x,
  boxplotWhiskersType="single",
  colorBy="dataset",
  colorScheme="JCO",
  graphOrientation="vertical",
  graphType="Boxplot",
  groupingFactors=list("dataset"),
  histogramBins=150,
  layoutTopology="1X3",
  legendColumns=3,
  legendPosition="top",
  legendScaleFontFactor=1.5,
  segregateVariablesBy=list("variable"),
  showViolinBoxplot=TRUE,
  smpLabelRotate=90,
  toolbarType="over",
  useOpenShapes=TRUE
)