Entering edit mode
Hi Sten,
I am assuming that you are using the latest development version of the
package since you are already setting the transcriptAnnotation
parameter (hint: always include the output of sessionInfo() when
asking for help). With this I tried to simplify the setting of labels
for GeneRegionTracks, and the idea is quite trivial:
rather than having to play with showId and geneSymbols, you can now
set everything with just one parameter, transcriptAnnotation. It can
take one of the values "symbol", "transcript" or "gene", and will use
the respective annotation for the labels. If not set at all , or if
set to "none", no labels are printed. You may wan to create your
GeneRegionTrack like this:
grtrack <- GeneRegionTrack(ensemblData, chromosome=12,
name="Transcripts", transcriptAnnotation="transcript",
background.title="#40464C", cex.group=0.7, cex.title=0.8,
fill="salmon")
plotTracks(grtrack)
Check out how setting the transcriptAnnotation parameter has an effect
on your plot:
plotTracks(grtrack, transcriptAnnotation="symbol")
plotTracks(grtrack, transcriptAnnotation="gene")
I will try to make this a bit clearer in the vignette. Btw, there are
several other ways to create a GeneRegionTrack, also from Ensembl
data. You may want to consult the vignette. Most of those assume that
you want to fetch data for a particular genomic region, so I am not
sure whether those make sense in your case.
Florian
From: Sten Ilmjärv
<sten.ilmjarv@gmail.com<mailto:sten.ilmjarv@gmail.com>>
Date: Tuesday, January 28, 2014 11:00 AM
To: Florian Hahne
<florian.hahne@novartis.com<mailto:florian.hahne@novartis.com>>
Subject: Gviz pacakge
plotTracks(list(itrack,gtrack,grtrack), from = min(ensemblData$start)
- 20000, to = max(ensemblData$end) + 20000)
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