Drawing a dotplotΒΆ

Section author: Gavin Huttley

>>> from cogent import LoadSeqs, DNA
>>> 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.

>>> aln = LoadSeqs("data/test.paml", moltype=DNA)
>>> 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.

>>> dp = dotplot.Display2D(seq1,seq2)
>>> filename = 'dotplot_example.pdf'
>>> dp.drawToPDF(filename)