Merge pull request #152 from Zethson/feature/review

Improve documentation

.gitignore

@@ -1,8 +1,165 @@
-dist/
-panpipes/__pycache__
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
 build/
-panpipes.egg-info
-*.pyc
+develop-eggs/
+dist/
+downloads/
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+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
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+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
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+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
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+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
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+# Flask stuff:
+instance/
+.webassets-cache
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+# Scrapy stuff:
+.scrapy
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+# Sphinx documentation
+docs/_build/
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+# PyBuilder
+.pybuilder/
+target/
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+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
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+# pipenv
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+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
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+#   in version control.
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+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
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+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
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+# SageMath parsed files
+*.sage.py
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+# Environments
+.env
+.venv
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+venv/
+ENV/
+env.bak/
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+# Rope project settings
+.ropeproject
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+# mkdocs documentation
+/site
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+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
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+# Pyre type checker
+.pyre/
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+.pytype/
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+# Cython debug symbols
+cython_debug/
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+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
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+# panpipes specific
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 .DS_Store

.readthedocs.yaml

@@ -1,32 +1,13 @@
-# .readthedocs.yaml
-# Read the Docs configuration file
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
 
-# Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
     python: "3.11"
-    # You can also specify other tool versions:
-    # nodejs: "19"
-    # rust: "1.64"
-    # golang: "1.19"
 
-# Build documentation in the "docs/" directory with Sphinx
 sphinx:
    configuration: docs/conf.py
 
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
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-
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
    install:
    - requirements: docs/requirements.txt

CHANGELOG.md

@@ -1,5 +1,5 @@
-Releases
-===========
+
+# Changelog
 
 ## [latest]
 
@@ -17,30 +17,30 @@ Releases
 ## v0.4.1
 
 ### added
+
 - added example multiome submission file 10X_h5
 - added example multiome submission file cellranger
 - workflows & tutorials for `qc_spatial`, `preprocess_spatial`, and `deconvolution_spatial` to readthedocs
 - tutorial for `vis`
 - added PCA parameters in pipeline_preprocess.py for PROT modality to fix issue #120
 - added full control of dimred params for all modalities in pipeline_preprocess.py
 - more info on custom genes format files added to documentation
-- parsing summary files for cellranger multi version < 7 
+- parsing summary files for cellranger multi version < 7
 - added checks for n_pcs in run_neighbors_method_choice
 - added filtering by HVF for atac
 
-
 ### fixed
 
 - changed typo in tutorial paths for clustering and deconvolution
-- fix io to read cellranger outs folder for atac. 
-- fixes to refmap workflow 
+- fix io to read cellranger outs folder for atac.
+- fixes to refmap workflow
 - typos & capitalization in the pipeline.yml files of `qc_spatial`, `preprocess_spatial`, and `deconvolution_spatial`, `vis`
-- remove `assay`, `sample_prefix`, and `modalities` parameters from the `qc_spatial` pipeline.yml 
+- remove `assay`, `sample_prefix`, and `modalities` parameters from the `qc_spatial` pipeline.yml
 - remove `sample_prefix` and `modalities` parameters from the `preprocess_spatial` pipeline.yml
 - fixed error in `preprocess_spatial` when `filtering: run: False`
     -> now able to run no filtering without needing to save the MuData in `filtered.data` before running the pipeline
 - fixed error in `vis`
-    - change PARAMS['custom_markers_minimal'] -> PARAMS['custom_markers']['files']['minimal']
+  - change PARAMS['custom_markers_minimal'] -> PARAMS['custom_markers']['files']['minimal']
 - fix to avoid rerunning HVF and explicitly check X layer before normalization in pipeline_preprocess.py
 - fix plotting of umaps after batch correction
 - fix fetching string scvi if present in mudata for wnn
@@ -49,54 +49,55 @@ Releases
 - fixed filtering HVG for rna
 - moved pynndescent to PyPi dependencies
 
-
 ### dependencies
 
 ## v0.4.0
 
 Big Change! the submission files for the `ingest` workflow have now changed! we require the paths to the Gene expression (RNA/GEX) and Protein (ADT) to have the following headers.
 
-
 | sample_id | rna_path    | rna_filetype | prot_path    | prot_filetype |
 | --------- | ----------- | ------------ | ------------ | ------------- |
 | sampleX   | path/to/rna | 10X_h5       | path/to/prot | 10x_h5        |
 |           |             |              |              |               |
 
-
 See tutorials for examples of submission files.
 
-
 ### added
+
 - merged PR #111:
   - LSI in panpipes_preprocess is run on the highly variable features
   - n_comp for LSI
+
 ### fixed
+
 - changed all instances of ADT into PROT
 - changed all instances of GEX to RNA
 - changed the params to fix plotting as mentioned in issue #41
 - typo in readme
 - set default seaborn <=0.12.2 to avoid issue #104, #126
 
-### dependencies
-
 ## v0.3.1
-- set default matplotlib<=3.7.3 to avoid issue #104. 
+
+- set default matplotlib<=3.7.3 to avoid issue #104.
 
 ## v0.3.0
+
 ### added
+
 - Spatial data analysis is now included in panpipes
-    - panpipes qc_spatial
-    - panpipes preprocess_spatial
-    - panpipes_deconvolution_spatial
+  - panpipes qc_spatial
+  - panpipes preprocess_spatial
+  - panpipes_deconvolution_spatial
 
 ### fixed
+
 - make sure columns from individual modalities that are not in the multimodal outer obs can be used to
 
 ### dependencies
+
 - additional dependencies: squidpy, cell2location, openpyxl
 
 ## v0.2.0
-- First public version of panpipes
-    - contains qc_mm, preprocess, intergration, clustering
-
 
+- First public version of panpipes
+- contains qc_mm, preprocess, intergration, clustering

README.md

@@ -1,42 +1,48 @@
 [![PyPI version](https://badge.fury.io/py/panpipes.svg)](https://badge.fury.io/py/panpipes)
-# Panpipes - multimodal single cell pipelines 
 
-Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion  
-Additional contributors: Sarah Ouologuem, Devika Agarwal, and Tom Thomas 
+# Panpipes - multimodal single cell pipelines
 
+## Overview
 
-**See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v1)**:  
-Panpipes: a pipeline for multiomic single-cell data analysis  
-Charlotte Rich-Griffin*, Fabiola Curion*, Tom Thomas, Devika Agarwal, Fabian J. Theis, Calliope A. Dendrou.  
-bioRxiv 2023.03.11.532085;  
-doi: https://doi.org/10.1101/2023.03.11.532085
+Panpipes is a set of computational workflows designed to automate multimodal single-cell and spatial transcriptomic analyses by incorporating widely-used Python-based tools to perform quality control, preprocessing, integration, clustering, and reference mapping at scale. 
+Panpipes allows reliable and customisable analysis and evaluation of individual and integrated modalities, thereby empowering decision-making before downstream investigations.
 
+**See our [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/) and our [preprint](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)**:  
 
-# Introduction
-These workflows use cgat-core pipeline software
+These workflows make use of [cgat-core](https://github.com/cgat-developers/cgat-core):
 
 Available workflows:
-1. "ingest" : for the ingestion of data and computation of QC metrics 
-2. "preprocess" : for filtering and normalising of each modality
-3. "integration" : integrate and batch correction using  single and multimodal methods
-4. "clustering" : cell clustering on single modalities
-5. "refmap" : transfer scvi-tools models from published data to your data
-6. "vis" : visualize metrics from other pipelines in the context of experiment metadata
-7. "qc_spatial" : for the ingestion of spatial transcriptomics (ST) data (Vizgen, Visium) and computation of QC metrics
-8. "preprocess_spatial" : for filtering and normalizing ST data
-9. "deconvolution_spatial" : for the cell type deconvolution of ST slides
-
-
-# Installation and configuration
-See [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html)
 
+1. "ingest" : Ingest data and compute quality control metrics
+2. "preprocess" : Filter and normalize per modality
+3. "integration" : Integrate and batch correct using single and multimodal methods
+4. "clustering" : Cluster cells per modality
+5. "refmap" : Map queries against reference datasets
+6. "vis" : Visualize metrics from other pipelines in the context of experiment metadata
+7. "qc_spatial" : Ingest spatial transcriptomics data (Vizgen, Visium) and compute quality control metrics
+8. "preprocess_spatial" : Filtering and normalize spatial transcriptomics data
+9. "deconvolution_spatial" : Deconvolve cell types of spatial transcriptomics slides
+
+## Installation and configuration
+
+See [installation instructions here](https://panpipes-pipelines.readthedocs.io/en/latest/install.html)
 
 Oxford BMRC Rescomp users find additional advice in [docs/installation_rescomp](https://github.com/DendrouLab/panpipes/blob/main/docs/installation_rescomp.md)
 
-# Releases
+## Releases
 
-`panpipes v0.4.0` is out [now](./CHANGELOG.md)! 
+`panpipes v0.4.0` is out [now](./CHANGELOG.md)!
 
 The `ingest` workflow now expects different headers for the RNA and Protein modalities.
 Check the example [submission file](https://github.com/DendrouLab/panpipes/blob/main/docs/usage/sample_file_qc_mm.md) and the [documentation](https://panpipes-pipelines.readthedocs.io/en/latest/usage/setup_for_qc_mm.html) for more detailed instructions.
 
+## Citation
+
+[Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis
+Fabiola Curion, Charlotte Rich-Griffin, Devika Agarwal, Sarah Ouologuem, Tom Thomas, Fabian J. Theis, Calliope A. Dendrou
+bioRxiv 2023.03.11.532085; doi: https://doi.org/10.1101/2023.03.11.532085](https://www.biorxiv.org/content/10.1101/2023.03.11.532085v2)
+
+## Contributors
+
+Created and Maintained by Charlotte Rich-Griffin and Fabiola Curion.
+Additional contributors: Sarah Ouologuem, Devika Agarwal, Lilly May, Kevin Rue-Albrecht.