Hello, I would like to plot a list of interesting genes (located on different chromosomes) on a genome. I extracted their genomic coordinates with biomaRt (see table below) and now I am looking for a way to send them all to some plotting function. So I have a matrix like this: chromosome_name start_position end_position strand band gene1 1 295038550 295099001 1 H6 gene2 2 8660648 8693244 -1 E3.1 gene3 X 880698 929632 -1 A3 gene4 4 84109214 84109545 1 C1.1 gene5 4 35964995 35982539 -1 C1.2 and now I want to plot all these genes on a genome to have a visual representation of their position. I've tried to do this with GenomeGraph, but it seems to allow only for extraction of all genes/transcripts etc. from a given region of a single chromosome, and not just from a user-supplied gene list. Could anyone please suggest a package/way to do this? thanks, jarek -- Jarek Bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Pl?n, Germany tel. +49 4522 763 287 | bryk at evolbio.mpg.de

On Wed, Oct 21, 2009 at 4:32 AM, Jarek Bryk <bryk@evolbio.mpg.de> wrote: > Hello, > > I would like to plot a list of interesting genes (located on different > chromosomes) on a genome. I extracted their genomic coordinates with biomaRt > (see table below) and now I am looking for a way to send them all to some > plotting function. > > So I have a matrix like this: > > chromosome_name start_position end_position strand band > gene1 1 295038550 295099001 1 H6 > gene2 2 8660648 8693244 -1 E3.1 > gene3 X 880698 929632 -1 A3 > gene4 4 84109214 84109545 1 C1.1 > gene5 4 35964995 35982539 -1 C1.2 > > and now I want to plot all these genes on a genome to have a visual > representation of their position. > > I've tried to do this with GenomeGraph, but it seems to allow only for > extraction of all genes/transcripts etc. from a given region of a single > chromosome, and not just from a user-supplied gene list. > > Could anyone please suggest a package/way to do this? > > You could try exporting them to a file (e.g. tab-separated) and viewing them in UCSC Genome Graphs (not to be confused with the R package). It shows data on an entire genome (across chromosomes). > thanks, > jarek > > -- > Jarek Bryk > Max Planck Institute for Evolutionary Biology > August Thienemann Str. 2 | 24306 Plön, Germany > tel. +49 4522 763 287 | bryk@evolbio.mpg.de > > _______________________________________________ > 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]]

One option would be to output your gene/co-ordinates in wig file format and upload them to the UCSC genome browser where they could be visualized. Have a look at the UCSC documentation for info on how to do this. That said there's probably an easier way... Paul. On Wed, Oct 21, 2009 at 12:32 PM, Jarek Bryk <bryk@evolbio.mpg.de> wrote: > Hello, > > I would like to plot a list of interesting genes (located on different > chromosomes) on a genome. I extracted their genomic coordinates with biomaRt > (see table below) and now I am looking for a way to send them all to some > plotting function. > > So I have a matrix like this: > > chromosome_name start_position end_position strand band > gene1 1 295038550 295099001 1 H6 > gene2 2 8660648 8693244 -1 E3.1 > gene3 X 880698 929632 -1 A3 > gene4 4 84109214 84109545 1 C1.1 > gene5 4 35964995 35982539 -1 C1.2 > > and now I want to plot all these genes on a genome to have a visual > representation of their position. > > I've tried to do this with GenomeGraph, but it seems to allow only for > extraction of all genes/transcripts etc. from a given region of a single > chromosome, and not just from a user-supplied gene list. > > Could anyone please suggest a package/way to do this? > > thanks, > jarek > > -- > Jarek Bryk > Max Planck Institute for Evolutionary Biology > August Thienemann Str. 2 | 24306 Plön, Germany > tel. +49 4522 763 287 | bryk@evolbio.mpg.de > > _______________________________________________ > 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 > -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland [[alternative HTML version deleted]]

The prepareGenomePlot() function in the quantsmooth package can be used to do that. Jan ________________________________ Hello, I would like to plot a list of interesting genes (located on different chromosomes) on a genome. I extracted their genomic coordinates with biomaRt (see table below) and now I am looking for a way to send them all to some plotting function. So I have a matrix like this: chromosome_name start_position end_position strand band gene1 1 295038550 295099001 1 H6 gene2 2 8660648 8693244 -1 E3.1 gene3 X 880698 929632 -1 A3 gene4 4 84109214 84109545 1 C1.1 gene5 4 35964995 35982539 -1 C1.2 and now I want to plot all these genes on a genome to have a visual representation of their position. I've tried to do this with GenomeGraph, but it seems to allow only for extraction of all genes/transcripts etc. from a given region of a single chromosome, and not just from a user-supplied gene list. Could anyone please suggest a package/way to do this? thanks, jarek -- Jarek Bryk Max Planck Institute for Evolutionary Biology August Thienemann Str. 2 | 24306 Plön, Germany tel. +49 4522 763 287 | bryk@evolbio.mpg.de _______________________________________________ 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]]