Entering edit mode
Hi Florian,
I don't mean to bug you, but I'm working on getting some figures put
together and it would be very handy to have this fix. If you point me
in
the right direction, I could take a stab at it. I know you're busy
with
other things. Thanks for you time.
Lance
Lance Parsons wrote:
> Fantastic. Not sure when this cropped up, but this will certainly
> help quite a bit. Let me know once you have a patch, I'd be happy
to
> test it.
>
> Lance
>
> Hahne, Florian wrote:
>> Jep, I think I know what is going on here. Damn factors in
>> data.frames
Will post a fix soon.
>> Florian
>>
>> From: Lance Parsons <lparsons@princeton.edu>> <mailto:lparsons@princeton.edu>>
>> Date: Wednesday 21 May 2014 17:53
>> To: "bioconductor@r-project.org
<mailto:bioconductor@r-project.org>"
>> <bioconductor@r-project.org <mailto:bioconductor@r-project.org="">>
>> Cc: Florian Hahne <florian.hahne@novartis.com>> <mailto:florian.hahne@novartis.com>>
>> Subject: Gviz Incorrect Labels on Features
>>
>> I have run into what appears to be a bug with GViz labels, though
>> perhaps I'm using the annotations incorrectly. The following
minimal
>> example seems to plot the correct features, but with the labels
mixed
>> up. I suspect the issue has to do with the sorting (or lack
thereof)
>> of the features in the GRanges list, however, I'm not sure of the
>> proper workaround. Any help would be appreciated.
>>
>> # Gviz annotation label mixup
>>
>> library(Gviz)
>> library(TxDb.Scerevisiae.UCSC.sacCer3.sgdGene)
>> txdb <- TxDb.Scerevisiae.UCSC.sacCer3.sgdGene
>> chr = 'chrVIII'
>> start=212535 - 500
>> end=214718 + 2000
>> grtrack = GeneRegionTrack(txdb, chromosome=chr, start=start,
end=end,
>> showId=TRUE, shape='fixedArrow')
>> grtrack@range
>> plotTracks(grtrack)
>>
>>
>> Here you can see that YHR054W-A should be plotted at 214508 and in
>> the forward direction. However, that is clearly not the case in
the
>> plot.
>>
>>
>> GRanges with 6 ranges and 7 metadata columns:
>> seqnames ranges strand | feature
>> id exon transcript gene symbol density
>> <rle> <iranges> <rle> | <character> <character> <character>
>> <character> <character> <character> <numeric>
>> [1] chrVIII [212510, 212704] + | CDS unknown
>> YHR052W-A_1 YHR052W-A YHR052W-A YHR052W-A 1
>> [2] chrVIII [214508, 214702] + | CDS unknown
>> YHR054W-A_1 YHR054W-A YHR054W-A YHR054W-A 1
>> [3] chrVIII [212535, 212720] - | CDS unknown
>> YHR053C_1 YHR053C YHR053C YHR053C 1
>> [4] chrVIII [213185, 214249] - | CDS unknown
>> YHR054C_1 YHR054C YHR054C YHR054C 1
>> [5] chrVIII [214533, 214718] - | CDS unknown
>> YHR055C_1 YHR055C YHR055C YHR055C 1
>> [6] chrVIII [215183, 217834] - | CDS unknown
>> YHR056C_1 YHR056C YHR056C YHR056C 1
>> ---
>> seqlengths:
>> chrVIII
>> NA
>>
>>
>>
>> --
>> Lance Parsons - Scientific Programmer
>> 134 Carl C. Icahn Laboratory
>> Lewis-Sigler Institute for Integrative Genomics
>> Princeton University
>>
>
> --
> Lance Parsons - Scientific Programmer
> 134 Carl C. Icahn Laboratory
> Lewis-Sigler Institute for Integrative Genomics
> Princeton University
>
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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