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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor

On Wed, Nov 5, 2008 at 12:53 PM, Camper (Chih-Wei Liu) < camper@cad.csie.ncku.edu.tw> wrote: > Thank you very much. > This package is very useful too. > However, if I want to plot all miRNAs in one chromosome, it doesn't work. > You might want to be a bit more specific here if you would like some suggestions. Sean > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Michael > Lawrence > Sent: Saturday, November 01, 2008 9:27 AM > To: Sean Davis > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] How to plot microRNA chromosome location > > On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > > <mailinglist.honeypot@gmail.com> wrote: > > > 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. > > > > > > > > Sorry for late reply here. In fact, there is an example in the rtracklayer > vignette that does pretty much exactly this, except with miRNA target > sites. > > Let me know if you need any more guidance. > > Thanks, > Michael > > > > > 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. > > > > See the rtracklayer package for help here. > > > > > 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 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

On Wed, Nov 5, 2008 at 9:53 AM, Camper (Chih-Wei Liu) < camper@cad.csie.ncku.edu.tw> wrote: > Thank you very much. > This package is very useful too. > However, if I want to plot all miRNAs in one chromosome, it doesn't work. > The Genome Graphs tool at UCSC (not to be confused with the GenomeGraphs R package) may be what you need. http://genome.ucsc.edu/cgi-bin/hgGenome?org=human You can upload a track to the genome browser using rtracklayer, and then import it into that tool using their web interface. > > -----Original Message----- > From: bioconductor-bounces@stat.math.ethz.ch > [mailto:bioconductor-bounces@stat.math.ethz.ch] On Behalf Of Michael > Lawrence > Sent: Saturday, November 01, 2008 9:27 AM > To: Sean Davis > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] How to plot microRNA chromosome location > > On Tue, Oct 28, 2008 at 2:59 AM, Sean Davis <sdavis2@mail.nih.gov> wrote: > > > On Mon, Oct 27, 2008 at 9:13 PM, Steve Lianoglou > > <mailinglist.honeypot@gmail.com> wrote: > > > 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. > > > > > > > > Sorry for late reply here. In fact, there is an example in the rtracklayer > vignette that does pretty much exactly this, except with miRNA target > sites. > > Let me know if you need any more guidance. > > Thanks, > Michael > > > > > 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. > > > > See the rtracklayer package for help here. > > > > > 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 > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > [[alternative HTML version deleted]]