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.. jupyter-execute::
:hide-code:
import set_working_directory
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``.
.. jupyter-execute::
from cogent3.app.io import get_data_store, load_json
loader = load_json()
seqs = loader("data/tp53.json")
dp = seqs.dotplot(name1="Macaque", name2="Marmoset", width=600)
dp.show()
.. jupyter-execute::
:hide-code:
outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-2.png"
dp.write(outpath)
Removing annotation tracks
--------------------------
.. jupyter-execute::
help(dp.remove_track)
Thus we could remove the left annotation track, for instance with
.. jupyter-execute::
dp.remove_track(left_track=True)
dp.show()
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