[BioC] Creating a graph showing Affy probe-set alignments along a small segment of chromosome

[Steve Lianoglou]

Hi,

On Sat, May 21, 2011 at 9:16 PM, Richard Student
<richard.a.student at gmail.com> wrote:
> Dear Bioconductor mailing list,
>
> If I have some CSV data in a file like this :
>
> Probe Set ID,Alignment Start,Alignment End,Strand,Gene Symbol
> 1380054_at,167415761,167416381,+,Phactr3
> 1368499_at,167437521,167502083,-,Sycp2
> 1378270_at,167504376,167504858,+,Ppp1r3d
> 1373656_at,167505691,167506150,-,Ppp1r3d
> 1395392_at,167508167,167508749,-,Ppp1r3d
>
> ...
>
> 1392332_at,170985205,170985581,+,Myt1
> 1375916_at,171012460,171013368,+,Pcmtd2
> 1374454_at,171013932,171014583,+,Pcmtd2
> 1398875_at,171021421,171022475,+,Polr3k
>
> ... and I want to make a nice graph showing where each probe set aligns
> along the region between 167400000 bp and 171000000 bp, where would be a
> good place to start?  I guess I would have to use a lot of low level
> plotting functions, but I would need to create a blank graph to begin with.
> what would be cool would be a thick vertical line on the left representing
> the chromosome and vertical lines to the right showing each probeset's
> alignment to the chromosome, with each line labeled by the ProbeSetID, gene
> Symbol and strand.

I'd thumb through the GenomeGraphs package (particularly its vignette):
http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs.html

Those plots are the transpose of what you are looking for (they're
"horizontal" where it sounds like you want yours to be "vertical"),
but maybe it'd do.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact