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Add some plotting functionality #22

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jamorrison
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None of this has been tested (at least by Jacob), so no idea if it works.
I have a sneaking suspicion that it won't work in the biscuiteer framework.

Two scripts have been added to inst/scripts for plotting examples (neither of
which uses the functions created in the R code directory). The rest of the
changes can be found in the R directory (and corresponding man page updates).
A few minor changes were made to fix some BiocCheck complaints as well.
@biobenkj
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We are holding off merging this in following conversations with @jamorrison and @ttriche until it is accepted as a BioC package. Then, this will go into devel.

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