Copy number variation plot
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Entering edit mode
4 weeks ago
Emmi • 0

enter image description here

Hi guys,

I am looking to create a plot like this. There has been a previous post on the forum on this with the plot from @bernatgel. I loved the solution but am unable to translate it to my data. Maybe someone knows?

I am looking to create this plot using karyoploteR.

My dataset looks like this (with made up examples below):

  • chromosome number
  • start: denotes start position of copy number variation
  • end: denotes the end position of the variation on the chromosome
  • ploidy
  • log2_ratio

    chromosome         start            end               ploidy
      1                 58865614        58865899          3.512352
      2                 14538784873     14538784998       3.512352
      4                 83948882        839497809         3.512352
      4                 82748427        827486789         3.512352
    

How do I adapt the code below, to work on my dataset?

kp <- plotKaryotype("hg19", plot.type = 4, labels.plotter = NULL, main="Random Data, 2Mb resolution", cex=3.2)
kpAddChromosomeNames(kp, srt=45, cex=2.2)
plotLRR(kp, tiles, ymin=-1, ymax=5, labels = NA,  points.col = "#AAAAAAAA", line.at.0 = FALSE, points.cex = 3, add.axis = FALSE)
plotCopyNumberCallsAsLines(kp, cn.calls = rr, ymin=-1, ymax=5, lwd=3, add.axis=FALSE, labels = NA)
kpAddChromosomeSeparators(kp, lwd=2, col = "#666666")
kpAxis(kp, ymin = -1, ymax=5, tick.pos = 0:4, cex=2.2)
kpAddLabels(kp, labels = "ploidy", cex=3, srt=90, pos=3, label.margin = 0.025)

Help would be greatly appreciated!

Copy-number-variation genomics • 239 views
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