How to modify centromere depiction in Gviz IdeogramTrack?
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Robert ▴ 10
@robert-21245
Last seen 17 months ago

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 • 290 views
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Robert Ivanek ▴ 700
@robert-ivanek-5892
Last seen 16 hours ago
Switzerland

Since version 1.31.8 you can set cenromereShape to "circle".

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