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.. jupyter-execute::
:hide-code:
import set_working_directory
Dotplot basics
==============
A technique (`Gibbs and McIntyre <https://www.ncbi.nlm.nih.gov/pubmed/5456129>`_) for comparing sequences. All ``cogent3`` sequence collections classes (``SequenceCollection``, ``Alignment`` and ``ArrayAlignment``) have a dotplot method.
.. todo:: Change dotplot ref to a citation
The method returns a drawable, as demonstrated below between unaligned sequences.
.. jupyter-execute::
from cogent3 import load_unaligned_seqs
seqs = load_unaligned_seqs("data/SCA1-cds.fasta", moltype="dna")
draw = seqs.dotplot()
draw.show()
.. jupyter-execute::
:hide-code:
outpath = set_working_directory.get_thumbnail_dir() / "plot_aln-dotplot-1.png"
draw.write(outpath)
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.
.. jupyter-execute::
draw = seqs.dotplot(name1="Human", name2="Mouse", window=8, threshold=8)
draw.show()
Displaying dotplot for the reverse complement
---------------------------------------------
.. jupyter-execute::
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.
.. jupyter-execute::
draw = seqs.dotplot(name1="Human", name2="Mouse", rc=True, title="SCA1", width=400)
draw.show()
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