R/nCircos.r

   1 #!/usr/bin/env littler
   2
   3 snps=read.csv('outside.csv')
   4 sdat=snps[,c(2,3,3,1,4,5,6,7)]
   5 #         rsID   Chr       Pos      A      C      G      T    sum
   6 #1  rs10500915 chr11  21753388 0.2891 0.4467 0.2643 0.0000 1.0001
   7
   8 out.file <- "nCircos.pdf";
   9 pdf(file=out.file, height=8, width=8);
  10
  11 library(RCircos)
  12 data(UCSC.HG19.Human.CytoBandIdeogram)
  13 RCircos.Set.Core.Components(cyto.info=UCSC.HG19.Human.CytoBandIdeogram, tracks.inside=4, tracks.outside=0, chr.exclude=c("chrX", "chrY"))
  14 RCircos.Set.Plot.Area()
  15 RCircos.Chromosome.Ideogram.Plot()
  16
  17 #RCircos.Tile.Plot(sdat, data.col=5, track.num=1, side="in",is.sorted=F)
  18 # Scatter Heatmap Heatmap
  19 RCircos.Heatmap.Plot(sdat, data.col=5, track.num=1, side="in",is.sorted=F)
  20 RCircos.Heatmap.Plot(sdat, data.col=6, track.num=2, side="in",is.sorted=F)
  21 RCircos.Heatmap.Plot(sdat, data.col=7, track.num=3, side="in",is.sorted=F)
  22 RCircos.Heatmap.Plot(sdat, data.col=8, track.num=4, side="in",is.sorted=F)
  23
  24 dev.off();