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.. jupyter-execute::
:hide-code:
import set_working_directory
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).
.. todo:: add citation for 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.
.. jupyter-execute::
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()
.. jupyter-execute::
:hide-code:
outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-coevolution.png"
coevo.drawable.write(outpath)
Display coevolution scores as a Violin plot
-------------------------------------------
.. jupyter-execute::
coevo = aln.coevolution(show_progress=False, drawable="violin")
coevo.drawable.show(width=300)
Display coevolution scores as a Boxplot
---------------------------------------
.. jupyter-execute::
coevo = aln.coevolution(show_progress=False, drawable="box")
coevo.drawable.show(width=300)
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