How to modify centromere depiction in Gviz IdeogramTrack?
1
0
Entering edit mode
Robert ▴ 10
@robert-21245
Last seen 2.8 years ago
United States

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 • 1.1k views
ADD COMMENT
0
Entering edit mode
Robert Ivanek ▴ 750
@robert-ivanek-5892
Last seen 12 months ago
Switzerland

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

ADD COMMENT

Login before adding your answer.

Traffic: 680 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6