Improve plotting.py

[zhang-ivy]

Description

This PR improves plotting functions in plotting.py. It does not alter any functions in plotlying.py

Todos

Notable points that this PR has either accomplished or will accomplish.

• Fix formatting of x and y axis labels
• Add argument (dpi) for controlling the resolution of the plot when saving
• Allow each edge to be labeled using the names of the nodes involved in the edge. This enhancement was only introduced for DDG plots. Handles both small molecules and protein mutations. Does not work for plotly-generated plots.
• Use the adjustText package to adjust data labels so that they are not overlapping
• Make the minimum and maximum axes of the plot larger

Questions

• Should we merge this into the main repo or should I just merge it in my fork since some of the changes may be specific to my needs I'm working on?

Status

• Ready to go

[pep8speaks]

Hello @zhang-ivy! Thanks for updating this PR. We checked the lines you've touched for PEP 8 issues, and found:

There are currently no PEP 8 issues detected in this Pull Request. Cheers! 🍻

Comment last updated at 2022-09-12 20:05:59 UTC

[zhang-ivy]

@mikemhenry @ijpulidos Can you review this and help me determine whether this a PR worth merging into the main repo or if I should just merge it into my own fork? Some of the changes I made may be specific to my own needs, though I did try to make the changes as general as possible. Specifically, the following change may be useful for others, but I implemented them only for the case that I'm interested in: plotting DDGs (and not DGs) using plotting.py (and not plotly.py):

• Allow each edge to be labeled using the names of the nodes involved in the edge. This enhancement was only introduced for DDG plots. Handles both small molecules and protein mutations. Does not work for plotly-generated plots.

Additionally, I didn't want the data labels to overlap, so I use the adjustText package to overcome that problem. I'm not sure if that package is something that we want to include as a dependency though.

[codecov]

Codecov Report

Merging #64 (00d176a) into main (76130d1) will decrease coverage by 2.51%.
The diff coverage is 0.00%.

❗ Current head 00d176a differs from pull request most recent head 31b89be. Consider uploading reports for the commit 31b89be to get more accurate results

[zhang-ivy]

@mikemhenry : What do you think about including adjustText as a dependency -- are you ok with it? Merging this PR would require it.

[mikemhenry]

@zhang-ivy thank you for pointing that out! I'm fine with it, given that
https://github.com/conda-forge/adjusttext-feedstock/blob/main/recipe/meta.yaml
it doesn't pull in anything extra and is on conda-forge! (I typed this out so that later I remember why we decided to do this)

[mikemhenry]

TODO

• add adjustText to conda env yaml

[zhang-ivy]

@mikemhenry : I think I'm done making changes to this! Could you add adjustText to the conda env yaml?

[mikemhenry]

@zhang-ivy yes! I can take care of this later today