Is there a way to plot multiple numeric genomic data files (bedgraph or wiggle doesn't matter) in the same plot? Not two plots side-by-side as they are commonly displayed, but actually in the same plot.
Is there a way to plot multiple numeric genomic data files (bedgraph or wiggle doesn't matter) in the same plot? Not two plots side-by-side as they are commonly displayed, but actually in the same plot.
You might try overlaying tracks at the UCSC genome browser (is that what you mean?). There's a method where the tracks are semi-transparent. Here are a couple of descriptions/tutorials:
http://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
http://davetang.org/muse/2012/03/15/ucsc-genome-browser-custom-overlap-tracks/
http://biowhat.ucsd.edu/homer/ngs/ucsc.html
http://tools-dev.genereg.net/?p=96
You could also try the GenomeGraphs package from bioconductor:
http://www.bioconductor.org/packages/release/bioc/html/GenomeGraphs.html
That has options for creating plots of data over genomic features - which means you can plot numerous things at once.
There's also those that thing that's done with the modencode data in GBrowse, whereby tracks are overlayed in a 3rd dimension, for instance in figure 1B of this article about Flybase. But I can't find any information on how to make those tracks in GBrowse (it may not be ready for prime time yet).
You might take a look at this Washington University site, an epigenome browser. There's a Nature Methods paper here. You could download the source and work it into a local installation.
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