[EMBOSS] Prettyplot options

david.bauer at bayerhealthcare.com david.bauer at bayerhealthcare.com
Mon Sep 22 12:10:04 UTC 2008


emboss-bounces at lists.open-bio.org schrieb am 22/09/2008 12:52:15:

> I've been trying to make a nice image of an alignment using prettyplot,
> but have failed to find the right set of options to get what I want.
> I need to get the whole alignment into one image (png), even if that
> ends up being very long and thin.  At the moment it always seems to
> paginate.

experiment with the option -residuesperline. 
If you set this large enough, you can squeeze the alignment to one page or 
even one row.

> I also need to get rid of all the text on the plot (including the
> program name and the list of options etc.).  I've tried all of the
> -gtitle -gsubtitle etc options, but there is some text I can't seem to
> shift.

with -nolist you can remove the run options which appear at the bottom of 
the plot.
But I have no idea how to remove the gtitle and gsubtitle completely.

> At a push I could get away with fixing either one of those two problems
> as I can then fix the other myself, but the combination of the two is
> making life difficult.
> Is there an option I'm missing or is this not possible with prettyplot?
> The nearest I got was:
> cat muscle.txt | prettyplot -graph png -nonumber -noname -consensus N
> -auto -sequences stdin -goutfile pretty.png -gdesc " " -gtitle " "
> -gsubtitle " "
> Cheers
> Simon.
> -- 
> Simon Andrews PhD
> Bioinformatics Group
> The Babraham Institute
> simon.andrews at bbsrc.ac.uk
> +44 (0) 1223 496463 
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