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Drawing a dotplot
=================
.. sectionauthor:: Gavin Huttley
.. doctest::
>>> from cogent import LoadSeqs
>>> from cogent.core import annotation
>>> from cogent.draw import dotplot
Load the alignment for illustrative purposes, I'll make one sequence a different length than the other and introduce a custom sequence annotation for a miscellaneous feature. Normally, those annotations would be on the unaligned sequences.
.. doctest::
>>> aln = LoadSeqs("data/test.paml")
>>> feature = aln.addAnnotation(annotation.Feature, "misc_feature",
... "pprobs", [(38, 55)])
>>> seq1 = aln.getSeq('NineBande')[10:-3]
>>> seq2 = aln.getSeq('DogFaced')
Write out the dotplot as a pdf file in the current directory note that seq1 will be the x-axis, and seq2 the y-axis.
.. doctest::
>>> dp = dotplot.Display2D(seq1,seq2)
>>> filename = 'dotplot_example.pdf'
>>> dp.drawToPDF(filename)
.. clean up
.. doctest::
:hide:
>>> import os
>>> os.remove('dotplot_example.pdf')
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