[BioC] Gviz Incorrect Labels on Features

[Hahne, Florian]

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 at princeton.edu<mailto:lparsons at 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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