Question

ggbio: integrate different plots

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andreucat91 • 0

@andreucat91-8929

Last seen 7.3 years ago

Spain

I am wondering if something like this (A and B):

is possible with `ggbio`.

ggbio • 1.5k views

ADD COMMENT • link updated 7.4 years ago by Michael Lawrence ★ 11k • written 7.4 years ago by andreucat91 • 0

score 0 · Answer 1 · 2016-12-12

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Michael Lawrence ★ 11k

@michael-lawrence-3846

Last seen 2.4 years ago

United States

It's possible with Tracks() to stack plots with a genomic X axis, assuming you could make them in the first place.

ADD COMMENT • link 7.4 years ago Michael Lawrence ★ 11k

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Thank you for your reply. To draw genes, what I use is the following:

p2 <- autoplot(txdb, which=genes_subset, label.color = "black", color = "brown", fill = "brown") +
  theme(panel.grid.major = element_blank(), panel.grid.minor = element_blank())

it draws gene structures including exons, introns, etc. How could I draw something like in the image? Just a rectangle with the gene names below.

ADD REPLY • link 7.4 years ago andreucat91 • 0

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Not sure. I don't think you can get just the genes from the TxDb directly. You'll need to extract them and pass them directly as a GRanges. As for the labeling, from reading the code, it might be possible to coerce that GRanges to a GRangesList, and labels might show up above the midpoint of the rectangles. I don't think there's any way to get them below. The author of ggbio has moved on to other things, so the package is not in a very good state right now.

ADD REPLY • link 7.4 years ago Michael Lawrence ★ 11k