TCGA Chart

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



Color Themes


{
   "binned":"true",
   "boxplotWhiskersType":"single",
   "colorBy":"dataset",
   "colorScheme":"JCO",
   "graphOrientation":"vertical",
   "graphType":"Boxplot",
   "groupingFactors":[
      "dataset"
   ],
   "histogramBins":"150",
   "layoutTopology":"1X3",
   "legendColumns":"3",
   "legendKeyBackgroundBorderColor":"rgba(0,0,0,0)",
   "legendKeyBackgroundColor":"rgba(0,0,0,0)",
   "legendPosition":"top",
   "legendTextScaleFontFactor":1.5,
   "segregateVariablesBy":[
      "variable"
   ],
   "showBoxplotOriginalData":"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,
  binned=TRUE,
  boxplotWhiskersType="single",
  colorBy="dataset",
  colorScheme="JCO",
  graphOrientation="vertical",
  graphType="Boxplot",
  groupingFactors=list("dataset"),
  histogramBins=150,
  layoutTopology="1X3",
  legendColumns=3,
  legendKeyBackgroundBorderColor="rgba(0,0,0,0)",
  legendKeyBackgroundColor="rgba(0,0,0,0)",
  legendPosition="top",
  legendTextScaleFontFactor=1.5,
  segregateVariablesBy=list("variable"),
  showBoxplotOriginalData=TRUE,
  smpLabelRotate=90,
  toolbarType="over",
  useOpenShapes=TRUE
)