Small bug fixes and docs improvements

[Lilly-May]

PR Checklist

• Documentation in docs is updated

Description of changes

Some small bug fixes and docs improvements which I noticed would be useful during the creation of the docs examples. I made the following changes:

• Changed pt.pl.dl.pairplot to a static method (and deleted the self parameter). Before, it was necessary to create a DialoguePlot object and then call the pairplot method using the created object. Now, the method can be called directly with pt.pl.dl.pairplot which matches the convention we have for creating plots so far. The example in the docs was updated as well.
• Fixed error message in subtract and add methods of PerturbationSpace object. Before, the error messages always printed that the reference_key is missing in adata.obs_names, although the test checks for the presence of the perturbations.
• Fixed error message for embedding_key in compute_control_diff of PerturbationSpace. Before, it printed that the reference key is missing instead of the embedding_key.
• Added target_col parameter in add and subtract methods of PerturbationSpace object. The reason for this is that the method compute_control_diff is called by add as well as subtract and if there’s no option to set target_col, it will always default to “perturbations” which would make it necessary to rename the column if it is not named that way in the adata by default. Since the default of the parameter is set to “perturbations” in add and subtract, nothing changes if the methods were already working with your data.
• Added docs parameter description for **kwargs for DBSCANSpace.computeand PseudobulkSpace.compute
• Set default values for cluster_key for KMeansSpace.compute and DBSCANSpace.compute directly in the method signature (to 'k-means' and 'dbscan' respectively). This saves checking if the parameter is none and, if so, setting it to the default value. Also, for DBSCAN, the docs claimed the default value is ‘k-means’, which I corrected to ‘dbscan’
• Added docs explanations for all parameters for pt.pl.scg.reg_mean_plot and pt.pl.scg.reg_var_plot

[codecov]

Codecov Report

Merging #409 (f0e24b0) into main (e2ff0f8) will not change coverage.
The diff coverage is 0.00%.

Additional details and impacted files

@@          Coverage Diff          @@
##            main    #409   +/-   ##
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  Coverage   0.00%   0.00%           
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  Files         40      40           
  Lines       4885    4882    -3     
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+ Misses      4885    4882    -3     

Files	Coverage Δ
pertpy/plot/_scgen.py	0.00% <ø> (ø)
pertpy/tools/_perturbation_space/_simple.py	0.00% <ø> (ø)
pertpy/plot/_dialogue.py	0.00% <0.00%> (ø)
...y/tools/_perturbation_space/_perturbation_space.py	0.00% <0.00%> (ø)

[Zethson]

Absolutely amazing! Really appreciate you digging through all of this and improving the minor things.

Thanks!