Sccellfie

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

What's Changed
* v0.4.1 by earmingol in https://github.com/earmingol/scCellFie/pull/4

- Quick fix for using full name imports (`sccellfie.plotting` instead of `sccellfie.pl`, and `sccellfie.stats` instead of `sccellfie.tl`)
- Update to readme

**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.4.0...v0.4.1

This version includes major changes that substantially improve scCellFie:

- Improved plots, their aesthetics, and labelling.
- Included new preprocessing for both matrices and AnnData objects.
- Completed docstrings for missing functions.
- Added communication module with special analyses for single-cell and spatial data.
- Included pattern analysis using Generalized Additive Models (GAM module).
- Added pseudo-bulks generation of cell types or other groups.
- Improve tests in general.

What's Changed
* v0.4.0 by earmingol in https://github.com/earmingol/scCellFie/pull/3

**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.3.0...v0.4.0

What's Changed
* Update to v0.3.0 by earmingol in https://github.com/earmingol/scCellFie/pull/2

**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.2.3...v0.3.0

Summary
Main change includes the implementation of a one-command pipeline to run scCellFie analysis (located in `sccellfie.sccellfie_pipeline.run_sccellfie_pipeline()`.

Other changes are harmonization of docstrings, minor bug fixes and changes in default parameters of a few functions.

What's Changed
* Update to v0.2.3 by earmingol in https://github.com/earmingol/scCellFie/pull/1

New Contributors
* earmingol made their first contribution in https://github.com/earmingol/scCellFie/pull/1

**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.2.2...v0.2.3

Commits included
earmingol
[Functions to manipulate GPR rules](https://github.com/earmingol/scCellFie/pull/1/commits/cdc71f34cfe9c8777dbf0df3de621dc9d0a4abb1)
[cdc71f3](https://github.com/earmingol/scCellFie/pull/1/commits/cdc71f34cfe9c8777dbf0df3de621dc9d0a4abb1)
earmingol
[DB - Removed indexes added after including new tasks](https://github.com/earmingol/scCellFie/pull/1/commits/cc91de993b0b81cfb21bce4cfec0c8813bb725bf)
[cc91de9](https://github.com/earmingol/scCellFie/pull/1/commits/cc91de993b0b81cfb21bce4cfec0c8813bb725bf)
earmingol
[Fixed bug when using X that is not a sparse array](https://github.com/earmingol/scCellFie/pull/1/commits/988080adabb59ceab1c80b496a89e482f817ac28)
[988080a](https://github.com/earmingol/scCellFie/pull/1/commits/988080adabb59ceab1c80b496a89e482f817ac28)
earmingol
[Speeded up generation of inputs and moved gpr functions](https://github.com/earmingol/scCellFie/pull/1/commits/2cdea2c321cc87ebbb7a81ee55ebfcab52bb0d3d)
[2cdea2c](https://github.com/earmingol/scCellFie/pull/1/commits/2cdea2c321cc87ebbb7a81ee55ebfcab52bb0d3d)
earmingol
[Faster generation of inputs, moved gpr functions, and added adata sub…](https://github.com/earmingol/scCellFie/pull/1/commits/ccd9285fc269c61014ccd533f11cb6f3f9ff1920)
[ccd9285](https://github.com/earmingol/scCellFie/pull/1/commits/ccd9285fc269c61014ccd533f11cb6f3f9ff1920)
earmingol
[Fixed bug when using X that is not a sparse array](https://github.com/earmingol/scCellFie/pull/1/commits/d485328e9673026854dec7f5014291e6565b1fdf)
[d485328](https://github.com/earmingol/scCellFie/pull/1/commits/d485328e9673026854dec7f5014291e6565b1fdf)
earmingol
[Corrected docstrings](https://github.com/earmingol/scCellFie/pull/1/commits/fa19ae1076a915f5f75ce5eafb6fab301ef2476f)
[fa19ae1](https://github.com/earmingol/scCellFie/pull/1/commits/fa19ae1076a915f5f75ce5eafb6fab301ef2476f)
earmingol
[Added stratified subsampling of adatas](https://github.com/earmingol/scCellFie/pull/1/commits/6c5d11f1432c363f090501939c4e4c4198313f27)
[6c5d11f](https://github.com/earmingol/scCellFie/pull/1/commits/6c5d11f1432c363f090501939c4e4c4198313f27)
earmingol
[Added differential analysis](https://github.com/earmingol/scCellFie/pull/1/commits/f636e2f0072a0622f7979c9c9dead88be509b912)
[f636e2f](https://github.com/earmingol/scCellFie/pull/1/commits/f636e2f0072a0622f7979c9c9dead88be509b912)
earmingol
[Added functions to explore/modify tasks DB](https://github.com/earmingol/scCellFie/pull/1/commits/8cd4b34cae5f9ee96f11c9195f6463448d93e7c8)
[8cd4b34](https://github.com/earmingol/scCellFie/pull/1/commits/8cd4b34cae5f9ee96f11c9195f6463448d93e7c8)
earmingol
[Minor modifications to work with new functions](https://github.com/earmingol/scCellFie/pull/1/commits/29e8e83d019feeb2779741f8784b9a842d906ba5)
[29e8e83](https://github.com/earmingol/scCellFie/pull/1/commits/29e8e83d019feeb2779741f8784b9a842d906ba5)
earmingol
[v0.2.3](https://github.com/earmingol/scCellFie/pull/1/commits/0cc9e7a010517f81a91b975de7142553f6ce2cce)
[0cc9e7a](https://github.com/earmingol/scCellFie/pull/1/commits/0cc9e7a010517f81a91b975de7142553f6ce2cce)
earmingol
[Added stratified subsampling of adata](https://github.com/earmingol/scCellFie/pull/1/commits/255550d516295107fd8feef2e64a35b2a70bf3d3)
[255550d](https://github.com/earmingol/scCellFie/pull/1/commits/255550d516295107fd8feef2e64a35b2a70bf3d3)
earmingol
[Improved docstring about alpha](https://github.com/earmingol/scCellFie/pull/1/commits/c0c92c2fcae41385d08f06956844226b6c8ac5d5)
[c0c92c2](https://github.com/earmingol/scCellFie/pull/1/commits/c0c92c2fcae41385d08f06956844226b6c8ac5d5)
earmingol
[Added volcano plot](https://github.com/earmingol/scCellFie/pull/1/commits/59ec650a054f7d3cef987cd6998354b0cdbfd714)
[59ec650](https://github.com/earmingol/scCellFie/pull/1/commits/59ec650a054f7d3cef987cd6998354b0cdbfd714)
earmingol
[Added normalization function based on total counts](https://github.com/earmingol/scCellFie/pull/1/commits/54b015822da057541a00e909333a45e746c2aa1a)
[54b0158](https://github.com/earmingol/scCellFie/pull/1/commits/54b015822da057541a00e909333a45e746c2aa1a)
earmingol
[Moved differential analysis plots to differential_results.py](https://github.com/earmingol/scCellFie/pull/1/commits/d78f1e247b98c5c0db353d6a7bf896bfa73e6ac1)
[d78f1e2](https://github.com/earmingol/scCellFie/pull/1/commits/d78f1e247b98c5c0db353d6a7bf896bfa73e6ac1)
earmingol
[Added plotting to imports](https://github.com/earmingol/scCellFie/pull/1/commits/a7af9ad4c4d66330be78dac3a1af9cb8a5cc956a)
[a7af9ad](https://github.com/earmingol/scCellFie/pull/1/commits/a7af9ad4c4d66330be78dac3a1af9cb8a5cc956a)
earmingol
[Removed output of dataframe to generate fig](https://github.com/earmingol/scCellFie/pull/1/commits/e5b24409e9f37cd32b68fe6f2a65d4ff9908e7c9)
[e5b2440](https://github.com/earmingol/scCellFie/pull/1/commits/e5b24409e9f37cd32b68fe6f2a65d4ff9908e7c9)
earmingol
[Removed output of dataframe to generate fig](https://github.com/earmingol/scCellFie/pull/1/commits/62b047c500ed815686236bf6a992761abfa683e5)
[62b047c](https://github.com/earmingol/scCellFie/pull/1/commits/62b047c500ed815686236bf6a992761abfa683e5)
earmingol
[Renamed x_label and y_label to xlabel and ylabel](https://github.com/earmingol/scCellFie/pull/1/commits/b5e839983a11faf26ce36e91c3a9efbeb9849c2b)
[b5e8399](https://github.com/earmingol/scCellFie/pull/1/commits/b5e839983a11faf26ce36e91c3a9efbeb9849c2b)
earmingol
[Added genes to correct in mouse](https://github.com/earmingol/scCellFie/pull/1/commits/8e643097f3e6a647fb520789504a68133c190928)
[8e64309](https://github.com/earmingol/scCellFie/pull/1/commits/8e643097f3e6a647fb520789504a68133c190928)
earmingol
[Mouse metabolic genes](https://github.com/earmingol/scCellFie/pull/1/commits/acae707599cb9fd4293a68653cf03222e7f9a6d4)
[acae707](https://github.com/earmingol/scCellFie/pull/1/commits/acae707599cb9fd4293a68653cf03222e7f9a6d4)
earmingol
[Added new pathways for hormones](https://github.com/earmingol/scCellFie/pull/1/commits/11d8dcf2d10da9078447e472f188582b5fd4d1a3)
[11d8dcf](https://github.com/earmingol/scCellFie/pull/1/commits/11d8dcf2d10da9078447e472f188582b5fd4d1a3)
earmingol
[Added/Changed gene nomenclatures](https://github.com/earmingol/scCellFie/pull/1/commits/c15b11167be49c44a43edafb872260cd7d9e1f74)
[c15b111](https://github.com/earmingol/scCellFie/pull/1/commits/c15b11167be49c44a43edafb872260cd7d9e1f74)
earmingol
[Newer versions](https://github.com/earmingol/scCellFie/pull/1/commits/6d6d58db7f630c24291c08edd0bd5286d737586f)
[6d6d58d](https://github.com/earmingol/scCellFie/pull/1/commits/6d6d58db7f630c24291c08edd0bd5286d737586f)
earmingol
[Added mouse genes to correct](https://github.com/earmingol/scCellFie/pull/1/commits/c9d6cb74408b248e4ee71e63902006861ff1869a)
[c9d6cb7](https://github.com/earmingol/scCellFie/pull/1/commits/c9d6cb74408b248e4ee71e63902006861ff1869a)
earmingol
[Added precomputed thresholds for mouse](https://github.com/earmingol/scCellFie/pull/1/commits/0841045bf76a224c71c37ad775e11a42757c1f0b)
[0841045](https://github.com/earmingol/scCellFie/pull/1/commits/0841045bf76a224c71c37ad775e11a42757c1f0b)
earmingol
[Added functions to transform gene names from ensembl to symbol](https://github.com/earmingol/scCellFie/pull/1/commits/71aa925879681c06be1b2d099a18d0ab230ee2fe)
[71aa925](https://github.com/earmingol/scCellFie/pull/1/commits/71aa925879681c06be1b2d099a18d0ab230ee2fe)
earmingol
[Added imports of missing functions](https://github.com/earmingol/scCellFie/pull/1/commits/8df8ce9e09263bd5eab805fdc8b808c77244de03)
[8df8ce9](https://github.com/earmingol/scCellFie/pull/1/commits/8df8ce9e09263bd5eab805fdc8b808c77244de03)
earmingol
[Added grid of violin plots](https://github.com/earmingol/scCellFie/pull/1/commits/51f11dc55648452b845dc459e4bf5948eae6385b)
[51f11dc](https://github.com/earmingol/scCellFie/pull/1/commits/51f11dc55648452b845dc459e4bf5948eae6385b)

**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.2.1...v0.2.2

- [Added code to fix gene names when they have alternative names.](https://github.com/earmingol/scCellFie/commit/faf1595f9842b8164fc9ce437607c1d2bd3c1d9c)