Re: [MUMmer-help] Adding icons to MUMmerplot output

[Adam P. <aph...@gm...>]

Hi Adam T.,
It's relatively easy to edit the gnuplot script (the .gp file
generated by mummerplot). The format is pretty self explanatory. You
can add some lines or points to that file and then generate the plot
by running gnuplot yourself on the .gp file. However, when you are
displaying an alignment of a multi-fasta file, the mummerplot script
takes care of translating the coordinate systems. For example, if you
have 2 contigs on the X-axis, mummerplot lays the second contig out on
the right of the first by simply adding the length of the first contig
to all the match coordinates of the second contig. If you want to plot
arbitrary features, you would either have to do this translation
yourself or hack the mummerplot script to take your features as input.

It's definitely a feature that's on my radar. I started working on a
mummerplot replacement (that supported .gff features) a few years back
but ran out of time and never finished. Will keep this in mind if I
ever pick it back up again.

Best,
-Adam P.


On Wed, Jan 23, 2013 at 5:53 AM, ADAM PAUL TARANTO
<apt...@st...> wrote:
> Does anyone know how to highlight the location of a sequence feature in MUMmerplot output?
>
> I am investigating an expanded gene family, paralogues occur on a number of different scaffolds. I have done an all against all comparison with Promer to identify syntenic regions around the duplicated genes, which was then visualised using mummerplot.
>
> It is difficult to tell where exactly paralogues occur in the graphic generated - So I would like to either A) add markers to the X/Y axises as a visual aide, or B) have mummerplot draw a mark where my gene occurs in self-self scaffold comparisons.
>
> Is it possible to achieve this by manually editing the gnu-plot script or .ps file output by MUMmerplot?
>
> Thanks,
>
> Adam
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