Parse data

[nbedanova]

Updating some plotting functions for Parse data and making them a bit more general to work with all the datasets in this repo.

Also added doublet filtering for Parse data.

[Copilot]

Pull Request Overview

This PR updates plotting functions and data import capabilities to work with Parse dataset, adds doublet filtering for Parse data, and makes existing plotting functions more flexible to work with multiple datasets.

Key changes:

• Added doublet detection dependency and filtering for Parse data
• Enhanced plotting functions with configurable parameters (condition names, center_data, mean aggregation)
• Made visualization functions more general with improved font sizing and formatting options

Reviewed Changes

Copilot reviewed 6 out of 9 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
pyproject.toml	Added doubletdetection package dependency
pf2rnaseq/imports.py	Added Parse data import with doublet filtering, added pandas import, updated copy operations
pf2rnaseq/figures/commonFuncs/plotPaCMAP.py	Updated PaCMAP visualization colors and legend positioning
pf2rnaseq/figures/commonFuncs/plotGeneral.py	Enhanced gene expression plotting with configurable parameters and improved cell count calculations
pf2rnaseq/figures/commonFuncs/plotFactors.py	Added component weight plotting, improved gene set scoring visualization, adjusted factor plot formatting
pf2rnaseq/factorization.py	Added negative value handling in condition correction and fixed rank indexing in R2X calculation

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[nbedanova]

@aarmey I fear this might have gotten too unruly to review. Let me know if you want me to split this up. It is a lot of smaller changes so was not sure best way to approach this.

[aarmey]

Code looks reasonable. For the csv file, I'd move it into a data subfolder and gzip compress it so that it doesn't show up as text.