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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