Question: ggbio: integrate different plots
0
gravatar for andreucat91
2.9 years ago by
Spain
andreucat910 wrote:

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

 

 

is possible with `ggbio`.

ggbio • 719 views
ADD COMMENTlink modified 2.9 years ago by Michael Lawrence11k • written 2.9 years ago by andreucat910
Answer: ggbio: integrate different plots
0
gravatar for Michael Lawrence
2.9 years ago by
United States
Michael Lawrence11k wrote:

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

ADD COMMENTlink written 2.9 years ago by Michael Lawrence11k

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 REPLYlink written 2.8 years ago by andreucat910

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 REPLYlink written 2.8 years ago by Michael Lawrence11k
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