Are there any packages available for making a karyogram with ideograms of each chromosome? I have looked at GenomeGraphs, Idiogram and a number of other packages but they seem like they have been designed to draw a single chromosome at a time. Ideally, I would like to produce pictures similar to those obtained from karyoview with a bit more programmatic control. I would like to draw ideograms of each chromosome and place a line next to the chromosomes to denote the location of some genes of interest. It would be optimal to be able to plot multiple lines next to the chromosomes to be able to illustrate multiple features (ie. one might be genes, a second might be copy number variations or single nucleotide polymorphisms). Thanks, Michael Gormley [[alternative HTML version deleted]]

You may have a look at the quantsmooth package, which has a function prepareGenomePlot() that can draw all idiagrams of a genome, and the functions grid.chromosome() and plotChromosome() that can plot ideograms at any location within a plot. Jan > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch [mailto:bioconductor- > bounces at stat.math.ethz.ch] On Behalf Of Michael Gormley > Sent: vrijdag 20 juni 2008 2:53 > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] karyogram > > Are there any packages available for making a karyogram with ideograms of > each chromosome? I have looked at GenomeGraphs, Idiogram and a number of > other packages but they seem like they have been designed to draw a single > chromosome at a time. Ideally, I would like to produce pictures similar > to > those obtained from karyoview with a bit more programmatic control. I > would > like to draw ideograms of each chromosome and place a line next to the > chromosomes to denote the location of some genes of interest. It would > be > optimal to be able to plot multiple lines next to the chromosomes to be > able > to illustrate multiple features (ie. one might be genes, a second might be > copy number variations or single nucleotide polymorphisms). > > Thanks, > Michael Gormley > > [[alternative HTML version deleted]] > > _______________________________________________ > 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