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 at 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
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 at r-project.org<mailto:bioconductor at="" r-project.org="">" <bioconductor at="" r-project.org<mailto:bioconductor="" at="" r-project.org="">>
Cc: Florian Hahne <florian.hahne at="" novartis.com<mailto:florian.hahne="" at="" 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 at 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
[cid:part1.07010103.00050306 at princeton.edu]
--
Lance Parsons - Scientific Programmer
134 Carl C. Icahn Laboratory
Lewis-Sigler Institute for Integrative Genomics
Princeton University
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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
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