Asteroid plot edges

[avivko]

Reference Issues/PRs

Fixes #167
Note: hoovering over the edges does not show the edge kind. @a-r-j Feel free to have a look at it!

What does this implement/fix? Explain your changes

• Adds the options to use show_edges without getting an error.
• Also now you could get rgba strings returned from the colour_edges function
• Also you can now set an alpha value for the edges through colour_edges (e.g. in the asteroid plot)

What testing did you do to verify the changes in this PR?

Ran it on JN and got a plot with edges without an error (attached)

[a-r-j]

Thanks for the PR!

Ah, yes, the line hover doesn't work on 2D scatters in Plotly AFAIK. If you're really desparate for it, one solution I've seen is to add transparent nodes on the midpoint of each line. https://stackoverflow.com/questions/46037897/line-hover-text-in-plotly

[codecov-commenter]

Codecov Report

Merging #170 (9be13eb) into master (8123f42) will increase coverage by 8.69%.
The diff coverage is 56.09%.

@@            Coverage Diff             @@
##           master     #170      +/-   ##
==========================================
+ Coverage   40.27%   48.96%   +8.69%     
==========================================
  Files          48       74      +26     
  Lines        2811     4254    +1443     
==========================================
+ Hits         1132     2083     +951     
- Misses       1679     2171     +492     

Impacted Files	Coverage Δ
graphein/grn/parse_trrust.py	37.77% <ø> (ø)
graphein/ml/diffusion.py	0.00% <0.00%> (ø)
graphein/ppi/edges.py	100.00% <ø> (ø)
graphein/ppi/graph_metadata.py	0.00% <ø> (ø)
graphein/ppi/graphs.py	54.34% <ø> (ø)
graphein/ppi/parse_biogrid.py	75.00% <ø> (ø)
graphein/ppi/visualisation.py	0.00% <0.00%> (ø)
graphein/protein/analysis.py	0.00% <0.00%> (ø)
graphein/protein/features/sequence/sequence.py	71.42% <0.00%> (+2.67%)	⬆️
graphein/protein/features/sequence/utils.py	28.00% <0.00%> (+3.00%)	⬆️
... and 59 more

---

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[a-r-j]

@avivko Happy to merge unless you want to try your hand at the edge labelling?

[avivko]

Thanks for the PR!

Ah, yes, the line hover doesn't work on 2D scatters in Plotly AFAIK. If you're really desparate for it, one solution I've seen is to add transparent nodes on the midpoint of each line. https://stackoverflow.com/questions/46037897/line-hover-text-in-plotly

Nah, it's fine. but I decided to add an option to display a legend that groups the edges by kind. This way you can click certain edge kinds away, which is neat/useful in my opinion. I'll push it in a jiffy.

[avivko]

@a-r-j Also, I see that one of your tests fails because of the ye old broken conda environment file.
I've made my own, simplified version of it that runs w/o resulting in conflicts, in case you want to give it a try:

cat graphein-gpu.yml 
name: graphein-gpu
channels:
  - salilab
  - schrodinger
  - pytorch
  - pyg
  - conda-forge
  - pytorch3d
  - defaults
dependencies:
  - python=3.8
  - pip
  - jupyter
  - ipywidgets
  - dssp
  - pymol
  - vmd-python
  - pytorch
  - torchvision
  - cudatoolkit=11.3
  - pytorch3d
  - pip:
    - graphein[all]
    - biovec

[a-r-j]

Great - that's a really nice solution.

Re the conda env, I'll check it out in another PR.

Thanks for the contribution! Appreciate the effort :)

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