Question: gviz: error when plotting BiomartGeneRegionTrack with"above"
gravatar for tonja.r
3.3 years ago by
United Kingdom
tonja.r40 wrote:

I want the annotation of the genes/transcripts appear above the transcripts and not on the left or right.

ensembl = useMart(biomart="ENSEMBL_MART_ENSEMBL", host="", path="/biomart/martservice", dataset="hsapiens_gene_ensembl")

biomTrack <- BiomartGeneRegionTrack(genome = "hg19", chromosome = "chr12", start = 57929124, end =58122355,name = "ENSEMBL", biomart = ensembl,transcriptAnnotation = "symbol")

displayPars(biomTrack) = list(showId=TRUE,stackHeight=0.5,background.title="transparent",fontcolor.title="black","above")

plotTracks(list(biomTrack), from = 57929124, to = 58122355) 


Unfortunately, I get this error:

Fehler in data.frame(txt = labs, x = cx, y = cy, stringsAsFactors = FALSE) :
  arguments imply differing number of rows: 109, 108

I do not get an error if I do not specify parameter.
How can I put the annotations to appear above the transcripts without an error?

ADD COMMENTlink modified 3.3 years ago by Robert Ivanek530 • written 3.3 years ago by tonja.r40
gravatar for Robert Ivanek
3.3 years ago by
Robert Ivanek530
Robert Ivanek530 wrote:

Thanks for pointing out this issue. The next devel release 1.11.16 should contain the fix.


ADD COMMENTlink written 3.3 years ago by Robert Ivanek530
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