v0.4.0

New features

• Added the s1_name and s2_name parameters to viz_imshow() and viz_spy() (#17).

  • You can use these parameters to adjust the sequence name shown on the x or y axis, respectively.

Performance

• Updated the default algorithm for finding shared k-mers between two strings. Rather than manually iterating through the suffix arrays produced by pydivsufsort.divsufsort() to identify shared k-mers, we now instead use pydivsufsort.common_substrings() -- which accomplishes the same thing much faster.

  • For example, creating a dot plot of two random 1 Mbp sequences (using k = 20) takes 26.52 seconds (max memory usage 563.09 MiB) using the old method and 2.16 seconds (max memory usage 617.53 MiB) using the new method.

  • The new method does have higher memory usage for long sequences -- to the point where some test cases crash Jupyter Notebook with the new method, but succeed (albeit after taking a long time) with the old method. If desired, you can choose to use the old method ("suff-only") by passing suff_only=True to the DotPlotMatrix() constructor.

• When using the old shared-k-mer-finding method ("suff-only") and creating a self dot plot (i.e. comparing a sequence with itself), wotplot will now detect if the sequences are identical and reuse the sequence's suffix array (rather than unnecessarily creating the same suffix array twice).

  • Note that there are still other, more dramatic ways to speed up the creation of self dot plots; this is a relatively small improvement.

Maintenance

• Breaking change: Removed the binary parameter of the DotPlotMatrix() constructor.

  • Now, all matrices are "not binary" by default. If you want to visualize a matrix in a binary way, you can now set binary=True when calling viz_imshow() or viz_spy() (this is analogous to the force_binary parameter in wotplot 0.3.0). Matrix visualization defaults to visualizing the matrix in color.

  • This change was motivated by benchmarking -- making the matrix "not binary" didn't seem to impact construction speed. It does impact visualization speed slightly, but the effects of this can be (entirely, I think?) offset by using binary=True during visualization.

  • Sorry for the breaking change. I think this makes the interface a lot more natural to use.

• Abstracted code from the benchmarking notebook to a separate file in the docs/ folder, and tried to tidy it up.

• Restructured and tested the SciPy version checking code.

• Additional tests.

• Added pytest-mock as a development dependency.

Bug fixes

• Fixed a bug where, if every single cell in the dot plot matrix was a match cell, the resulting dot plot would be empty (#19).

Documentation

• Add better documentation to wotplot._make._get_row() and wotplot._make._make().

• Various updates to the README, tutorial notebook, and benchmarking notebook.

• The tutorial now includes a more complex example of creating a grid of dot plots. The example (shown below) creates a grid figure comparing all pairs of sequences with each other.

Fancy screenshot of a grid of dot plots from the tutorial

v0.3.0

New features

• Added the ability to visualize not-binary matrices in color using viz_spy() (#11).

  • In support of this new feature: added the force_binary, nbcmap, and draw_order parameters to viz_spy().

• Added verbose parameters to viz_spy() and viz_imshow().

Documentation

• Various updates to the README, tutorial, and benchmarking notebooks.
• Fixed the docstring of wotplot._make._fill_match_cells().
• Small improvements to the docstring of wotplot.viz_spy().

Maintenance

• Added more tests (mostly focusing on checking the visualization functions' verbose logging).
• Various small code improvements (abstracting repeated bits of code, etc.)

Fancy screenshot of a large multicolor dotplot matrix

v0.2.0

Documentation

• Various improvements and updates to the README and notebooks.

Performance

• Used the method proposed at https://bioinformatics.stackexchange.com/a/3585 to speed up and simplify the internal function used for reverse-complementing.

v0.1.0: Initial release

DOC: binary=False / vals updates in tutorial