In ggbio, plot transcripts from a TxDb with gene labels
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grp2009 • 0
@grp2009-11057
Last seen 4.8 years ago

I am trying to change the labels in ggbio's autoplot output (specifically, when the input is a TxDb) so that the transcripts are labelled with the corresponding gene symbol. What I'm starting with is the following code:

library(ggbio)
library(GenomicRanges)
wh <- GRanges(seqnames='chr18',
        ranges=IRanges(start=11688900,end=11885700)
)
library(TxDb.Hsapiens.UCSC.hg19.knownGene)
txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
autoplot(txdb, which = wh)

The output is very nice, but the transcripts are labelled with transcript identifiers such as uc002kqh.3, etc.  I would like to replace these labels with gene symbols, but despite poring through the documentation I can see no way to do this. Any ideas?

ggbio • 1.4k views
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@michael-lawrence-3846
Last seen 2.4 years ago
United States

The TxDb objects do not contain gene symbols (go figure). You could use an OrganismDb object (e.g., from the Homo.sapiens package). Then ggbio will use gene symbols by default.

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