Question: How to modify centromere depiction in Gviz IdeogramTrack?
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gravatar for Robert
4 months ago by
Robert10
Robert10 wrote:

I visualize my NGS data using the Gviz library. I can create and plot a IdeogramTrack with the following code.

library(Gviz)

cyto.bands <- data.frame(chrom = rep("chrI", 4),
                         chromStart = c(0, 148071, 151524, 154977),
                         chromEnd = c(148071, 151524, 154977, 230218),
                         name = c(NA, "CEN1", "CEN1", NA),
                         gieStain = c("gneg", "acen", "acen", "gneg"))

ideogram.track <- IdeogramTrack(chromosome = "chrI", genome = "sacCer3", bands = cyto.bands)

plotTracks(ideogram.track, from = 180e3, to = 220e3)

In the resulting plot, the centromere is depicted as two head-to-head triangles with brownish red filling (see e.g. here for an example).

Is it possible to change how the centromere is depicted? Can one change the fill color? Can one change the shape (e.g. one filled circle instead of the triangles)?

gviz • 85 views
ADD COMMENTlink written 4 months ago by Robert10
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