Evaluating coevolution¶
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¶
[1]:
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.show()
Display coevolution scores as a Violin plot¶
[2]:
coevo = aln.coevolution(show_progress=False, drawable='violin')
coevo.show(width=300)
Display coevolution scores as a Boxplot¶
[3]:
coevo = aln.coevolution(show_progress=False, drawable='box')
coevo.show(width=300)