What's Changed
* v0.4.2 by earmingol in https://github.com/earmingol/scCellFie/pull/6
* This PR includes a series of improvements:
- Network plot for visualizing cell-cell communication
- Added function to select markers from TF-IDF results
- Harmonized outputs across differential analyses
- Implemented subsampling in differential analysis
- Added beeswarm plot for visualizing results from differential analysis
- Added information about cell fraction using determinant genes of metabolic reactions
- Added `tight_layout` parameter to select whether using it or not in plots
- Improved a few docstrings
- Fixed minor bugs
* Update to phenylalanine-associated tasks by earmingol in https://github.com/earmingol/scCellFie/pull/7
* Merged Phenylalanine to phenylacetyl-L-glutaminate onto Phenylalanine to phenylacetaldehyde
Phenylalanine to phenylacetyl-L-glutaminate only had reactions ALDD19xr (r0545), PHYCBOXL, and PEAMNO, which are the same ones defining Phenylalanine to phenylacetaldehyde. The latter only had PHYCBOXL, and PEAMNO here, which is incomplete.
Reactions that should be in Phenylalanine to phenylacetyl-L-glutaminate are ALDD19xr (r0545), PACCOAL and PHACCOAGLNAC. However, the last two are not linked to human/mouse enzymes and seem to happen only in microbes (https://pubmed.ncbi.nlm.nih.gov/36549300/).

For this reason, only keeping the Phenylalanine to phenylacetaldehyde task, including ALDD19xr (r0545), PHYCBOXL, and PEAMNO reactions.
**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.4.1...v0.4.2