Question: Gviz - ReverseStrand incompatible with just.group="above"
0
gravatar for romain.fenouil
3.1 years ago by
romain.fenouil10 wrote:

Hello there, sorry for spamming the forum about Gviz but it's a great library and I really want to use it.

I think there is a small bug when trying to plot an annotation track with reversed strand and ID names on top of annotations.

> annoTrack <- BiomartGeneRegionTrack(genome="HG19", name="ENSEMBL", symbol="PPM1F")
> plotTracks(annoTrack, showId=TRUE, reverseStrand=FALSE, just.group="above") # works fine
> plotTracks(annoTrack, showId=TRUE, reverseStrand=TRUE) # works fine
> plotTracks(annoTrack, showId=TRUE, reverseStrand=TRUE, just.group="above")
Error in validObject(x) : 
  invalid class “IRanges” object: 'width(x)' cannot contain negative integers

Is this behaviour reproducible ?

Thank you for your help.

Romain.

gviz • 595 views
ADD COMMENTlink modified 3.1 years ago by Robert Ivanek590 • written 3.1 years ago by romain.fenouil10

It is actually also the case for just.group="below". Other values "left" and "right" work fine.

ADD REPLYlink written 3.1 years ago by romain.fenouil10
Answer: Gviz - ReverseStrand incompatible with just.group="above"
0
gravatar for Robert Ivanek
3.1 years ago by
Robert Ivanek590
Switzerland
Robert Ivanek590 wrote:

Thanks for the reporting this bug. I fixed it in the release 1.14.3 and devel version 1.15.3.

Best

Robert

ADD COMMENTlink written 3.1 years ago by Robert Ivanek590
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