Add examples to plotting functions

[namsaraeva]

Added plots:

• sccoda
• tasccoda - ete3 problems
• augur - long runtime
• enrichment
• milo - last two plotting methods throw errors
• mixscape

[namsaraeva]

Decided to merge the issues #458 and #447 to avoid possible conflicts in the future since I am editing docstrings.

[namsaraeva]

A little bit more context to the tasscoda issue:

tasccoda.plot_draw_tree(mdata, tree="lineage") fails with Import Error: to use tasscoda please install ete3 with pip install ete3

even though ete3 is installed (see session info below), so I couldn't generate example plots for all tasscoda plotting functions.

session_info.txt

[namsaraeva]

Augur example code:

import pertpy as pt
adata = pt.dt.bhattacherjee()
ag_rfc = pt.tl.Augur("random_forest_classifier")

data_15 = ag_rfc.load(adata, condition_label="Maintenance_Cocaine", treatment_label="withdraw_15d_Cocaine")
adata_15, results_15 = ag_rfc.predict(data_15, random_state=None, n_threads=4)
adata_15_permute, results_15_permute = ag_rfc.predict(data_15, augur_mode="permute", n_subsamples=100, random_state=None, n_threads=4)

data_48 = ag_rfc.load(adata, condition_label="Maintenance_Cocaine", treatment_label="withdraw_48h_Cocaine")
adata_48, results_48 = ag_rfc.predict(data_48, random_state=None, n_threads=4)
adata_48_permute, results_48_permute = ag_rfc.predict(data_48, augur_mode="permute", n_subsamples=100, random_state=None, n_threads=4)
pvals = ag_rfc.predict_differential_prioritization(augur_results1=results_15, augur_results2=results_48, permuted_results1=results_15_permute, permuted_results2=results_48_permute)
ag_rfc.plot_dp_scatter(pvals)

fails too.

pvals = ag_rfc.predict_differential_prioritization(augur_results1=results_15, augur_results2=results_48, permuted_results1=results_15_permute, permuted_results2=results_48_permute) can't be calculated due to TypeError: Passing a set as an indexer is not supported. Use a list instead.

See session info in the comment above.

[namsaraeva]

Milo:

Couldn't find the reason for this error either

[Zethson]

Great! Generally looks good. Let's fix the issues and finish the docstrings

[codecov]

Codecov Report

Attention: 2 lines in your changes are missing coverage. Please review.

Comparison is base (d49872c) 63.99% compared to head (8a37d15) 64.07%.
Report is 15 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #511      +/-   ##
==========================================
+ Coverage   63.99%   64.07%   +0.07%     
==========================================
  Files          43       43              
  Lines        4969     4982      +13     
==========================================
+ Hits         3180     3192      +12     
- Misses       1789     1790       +1     

Files	Coverage Δ
pertpy/data/__init__.py	100.00% <ø> (ø)
pertpy/data/_dataloader.py	100.00% <ø> (ø)
pertpy/data/_datasets.py	100.00% <ø> (ø)
pertpy/plot/_coda.py	100.00% <ø> (ø)
pertpy/tools/_coda/_base_coda.py	56.08% <ø> (ø)
pertpy/tools/_dialogue.py	13.70% <ø> (ø)
pertpy/tools/_distances/_distances.py	88.60% <100.00%> (ø)
pertpy/tools/_enrichment.py	52.02% <ø> (ø)
pertpy/tools/_milo.py	49.00% <ø> (ø)
pertpy/tools/_mixscape.py	79.80% <ø> (-0.20%)	⬇️
... and 4 more

[Zethson]

Thank youu!!

Could we please remove the TODOs for adding the missing previews? They'll already render which isn't pretty.

I'm confident that @Lilly-May or whoever is going to add them will be able to identify them or they can look at the state of this PR before merging