[BioC] How to plot microRNA chromosome location

[laurent]

On Thu, 2008-11-06 at 01:36 +0800, Camper (Chih-Wei Liu) wrote:
> I have tried GenomeGraphs package to plot chromosome miRNA maps.
> I got the results.
> 
> However, there still two questions I want to ask.
> 1. Is there any package be able to plot chromosomes at one time.
>   (Actually, I can do them all one by one and combine them manually.)

I assume that you mean all chromosomes on one figure.
It does not seem currently possible at the moment (as gdPlot calls
"grid.newpage()" in all cases). I had code to plot karyotypes-sort of
plots somewhere, let me see if I can find it back and send it.

> 2. Is GenomeGraphs package be able to draw mouse chromosome maps or any
> other species?

The man page for makeIdeogram() / Ideogram-class state that only human
chromosomes are supported. Having that extended to other organisms would
be a matter of letting one specify cytobands and chromosomes for
arbitray organisms (easier written here than done, there were several
way of specify cytobands/centromere/telomere regions last time I looked)



L.



> Thank you for answering.
> 
> -camper
> 
> ==================================================
> Camper Chih-Wei Liu
> National Cheng Kung University, Tainan, Taiwan
> Department of Computer Science and Information Engineering
> Intelligent Information Retrieval Lab: IIR Lab 
> camper at cad.csie.ncku.edu.tw
> 
> -----Original Message-----
> From: Steve Lianoglou [mailto:mailinglist.honeypot at gmail.com] 
> Sent: Tuesday, October 28, 2008 9:14 AM
> To: Camper (Chih-Wei Liu)
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] How to plot microRNA chromosome location
> 
> Hi,
> 
> On Oct 27, 2008, at 6:39 PM, Camper (Chih-Wei Liu) wrote:
> 
> > Hi all,
> >
> >
> >
> > I have check some useful packages to plot gene chromosome  
> > information like
> > gene plotter, ideogram and GenomeGraphs.
> >
> > However, I don't know how to plot microRNA (miRNA) chromosome  
> > location.
> >
> > I would like to see the distribution of some miRNAs in the genome.
> >
> >
> >
> > I have known the miRNA chromosome info.
> >
> > miRNA name           chromosome           start           end
> >
> > hsa-miR-130b            22                             20337592      
> > 20337673
> >
> > hsa-miR-33a              22                             40626894
> > 40626962
> >
> > hsa-miR-15b              3                              161605069
> > 161605166
> >
> > .
> >
> >
> >
> > Is there any packages that I provide the location and plotting it out?
> 
> You could create a custom track and upload it to the UCSC genome  
> browser.
> 
> It looks like you got your info about 90% the way to GFF format:
> 
> http://genome.ucsc.edu/FAQ/FAQformat#format3
> 
> You could tweak your info a bit, then write.table your way to a file  
> you can upload as a UCSC custom track.
> 
> Is that good enough, or were you looking for something more? And if  
> so, what? There's the GenomeGraphs library, which is pretty slick, but  
> I'm not sure if that's really what you're after:
> 
> http://bioconductor.org/packages/release/bioc/html/GenomeGraphs.html
> 
> Hope that helps,
> 
> -steve
> 
> --
> Steve Lianoglou
> Graduate Student: Physiology, Biophysics and Systems Biology
> Weill Cornell Medical College of Cornell University
> 
> http://cbio.mskcc.org/~lianos
> 
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