Dotplot basics

Note

These docs now use the new_type core objects via the following setting.

import os

# using new types without requiring an explicit argument
os.environ["COGENT3_NEW_TYPE"] = "1"

A technique (Gibbs and McIntyre) for comparing sequences. All cogent3 sequence collections classes (SequenceCollection, Alignment) have a dotplot method.

The method returns a drawable, as demonstrated below between unaligned sequences.

from cogent3 import load_unaligned_seqs

seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna")
draw = seqs.dotplot()
draw.show()

If sequence names are not provided, two randomly chosen sequences are selected (see below). The plot title reflects the parameter values for defining a match. window is the size of the sequence segments being compared. threshold is the number of exact matches within window required for the two sequence segments to be considered a match. gap is the size of a gap between adjacent matches before merging.

Modifying the matching parameters

If we set window and threshold to be equal, this is equivalent to an exact match approach.

draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8)
draw.show()

Displaying dotplot for the reverse complement

draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True)
draw.show()

Note

clicking on an entry in the legend turns it off

Setting plot attributes

I’ll modify the title and figure width.

draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400)
draw.show()