Dotplot with annotated sequences¶

If sequences in a dotplot have been annotated, the dotplot() method returns an AnnotatedDrawable.

Reloading from json¶

The data file, tp53.json, was created from a query of ensembl for one-to-one orthologs of human TP53 between Human, Macaque, Orangutan and Marmoset. The resulting sequences were annotated with the location of the CDS for the canonical transcript, then the SequenceCollection was saved as json using cogent3.app.write_json.

[1]:

from cogent3.app.io import load_json, get_data_store

loader = load_json()
seqs = loader("../data/tp53.json")
dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600)
dp

[1]:

<cogent3.draw.drawable.AnnotatedDrawable at 0x112d21fa0>

Removing annotation tracks¶

[2]:

help(dp.remove_track)

Help on method remove_track in module cogent3.draw.drawable:

remove_track(left_track=False, bottom_track=False) method of cogent3.draw.drawable.AnnotatedDrawable instance
    Parameters
    ----------
    left_track : bool
        the left track is removed
    bottom_track : bool
        the bottom track is removed

Thus we could remove the left annotation track, for instance with

dp.remove_track(left_track=True)

For some reason, the display of this result is broken on RTD so we don’t do it here.