Sccellfie

What's Changed
* DB update - Phenylalanine pathways by earmingol in https://github.com/earmingol/scCellFie/pull/8
* v0.4.3 by earmingol in https://github.com/earmingol/scCellFie/pull/9
* This PR includes the following changes:
- Optimization to the `sccellfie.preprocessing.adata_utils.stratified_subsample_adata()` function.
- Update to docstrings
- Modified saving of CCC network plot (`sccellfie.plotting.communication.plot_communication_network()`).
- Implemented functions to export results for scCellFie Metabolic Task Visualizer (see `sccellfie.reports.summary`)
- Implemented radial plots (`sccellfie.plotting.radial_plot.create_radial_plot()`)
- Updated requirements in `setup.py`


**Full Changelog**: https://github.com/earmingol/scCellFie/compare/v0.4.2...v0.4.3

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

EDIT
**Phenylalanine-associated tasks were rolled back by earmingol in 8 and modified as follows:**

Changes in https://github.com/earmingol/scCellFie/pull/7 were incorrect.

Phenylalanine to phenylacetyl-L-glutaminate only had reactions ALDD19xr (r0545), PHYCBOXL, and PEAMNO since there are no GPR rules for PACCOAL and PHACCOAGLNAC.


For this reason, Phenylalanine to phenylacetyl-L-glutaminate was renamed to Phenylalanine to phenylacetate (via phenylacetaldehyde)

*These changes to phenylalanine tasks are not contained in this release source code, containing 7 instead. For lastest version check the main branch*


**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)