Coevolution analysis

A method on the alignment provides an interface to the simpler (and yet robust and fast) methods for estimating coevolution. The default measure is normalised mutual information (NMI).

Display coevolution as a heatmap

Using the drawable argument causes the returned object to have a drawable attribute (type Drawable which has show() and write() methods), for the corresponding plot types – a heatmap in this case.

from cogent3 import load_aligned_seqs

aln = load_aligned_seqs("data/brca1.fasta", moltype="dna")
aln = aln.no_degenerates(motif_length=3)
aln = aln.get_translation()
aln = aln[:100]  # for compute speed in testing the documentation
coevo = aln.coevolution(show_progress=False, drawable="heatmap")
coevo.drawable.show()

Display coevolution scores as a Violin plot

coevo = aln.coevolution(show_progress=False, drawable="violin")
coevo.drawable.show(width=300)

Display coevolution scores as a Boxplot

coevo = aln.coevolution(show_progress=False, drawable="box")
coevo.drawable.show(width=300)