Counting gaps per sequence

We have several different ways of counting sequence gaps, and of visualising the results. By default, the count_gaps_per_seq() method returns a matrix of counts without the ability to visualise the results. When setting the argument unique=True, the counts are for gaps uniquely induced by each sequence. This can be a useful indicator of highly divergent sequences.

from cogent3 import load_aligned_seqs


aln = load_aligned_seqs('../../data/brca1.fasta', moltype='dna')

counts = aln.count_gaps_per_seq(unique=True)
counts

FlyingFox	DogFaced	FreeTaile	LittleBro	TombBat	RoundEare	FalseVamp	LeafNose	Horse	Rhino	Pangolin	Cat	Dog	Llama	Pig	Cow	Hippo	SpermWhale	HumpbackW	Mole	Hedgehog	TreeShrew	FlyingLem	Galago	HowlerMon	Rhesus	Orangutan	Gorilla	Human	Chimpanzee	Jackrabbit	FlyingSqu	OldWorld	Mouse	Rat	NineBande	HairyArma	Anteater	Sloth	Dugong	Manatee	AfricanEl	AsianElep	RockHyrax	TreeHyrax	Aardvark	GoldenMol	Madagascar	Tenrec	LesserEle	GiantElep	Caenolest	Phascogale	Wombat	Bandicoot
0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	3	0	0	0	0	0	3	0	3	21	0	0	0	0	0	0	57	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	0	6	0	6	0	0	0	0

Plotting counts of unique gaps

There are three plot types supported. In all cases, placing the mouse pointer over a data point will show hover text with the sequence name.

Displaying unique gaps as a bar chart

counts = aln.count_gaps_per_seq(unique=True, drawable='bar')
counts.show(width=500)

Displaying unique gaps as a violin plot

counts = aln.count_gaps_per_seq(unique=True, drawable='violin')
counts.show(width=300, height=500)

Displaying unique gaps as a box plot

counts = aln.count_gaps_per_seq(unique=True, drawable='box')
counts.show(width=300, height=500)