adding documentation

cantinilab · Aug 6, 2024 · 1a9d883 · 1a9d883
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diff --git a/Makefile b/Makefile
@@ -86,6 +86,8 @@ release:          ## Create a new tag for release.
 	@git tag $${TAG}
 	@git push -u origin HEAD --tags
 	@echo "Github Actions will detect the new tag and release the new version."
+	@mkdocs gh-deploy
+	@echo "also pushed the documentation website"
 
 .PHONY: docs
 docs:             ## Build the documentation.

diff --git a/README.md b/README.md
@@ -1,35 +1,73 @@
-# grnndata
+# GRnnData
 
 [![codecov](https://codecov.io/gh/cantinilab/GRnnData/branch/main/graph/badge.svg?token=GRnnData_token_here)](https://codecov.io/gh/cantinilab/GRnnData)
 [![CI](https://github.com/cantinilab/GRnnData/actions/workflows/main.yml/badge.svg)](https://github.com/cantinilab/GRnnData/actions/workflows/main.yml)
-[![DOI](https://zenodo.org/badge/731236048.svg)](https://zenodo.org/doi/10.5281/zenodo.10573141)
+[![PyPI version](https://badge.fury.io/py/GRnnData.svg)](https://badge.fury.io/py/benGRN)
+[![Documentation Status](https://readthedocs.org/projects/GRnnData/badge/?version=latest)](https://GRnnData.readthedocs.io/en/latest/?badge=latest)
+[![Downloads](https://pepy.tech/badge/GRnnData)](https://pepy.tech/project/GRnnData)
+[![Downloads](https://pepy.tech/badge/GRnnData/month)](https://pepy.tech/project/GRnnData)
+[![Downloads](https://pepy.tech/badge/GRnnData/week)](https://pepy.tech/project/GRnnData)
+[![GitHub issues](https://img.shields.io/github/issues/cantinilab/GRnnData)](https://img.shields.io/github/issues/cantinilab/GRnnData)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![DOI](https://img.shields.io/badge/DOI-10.1101%2F2024.07.29.605556-blue)](https://doi.org/10.1101/2024.07.29.605556)
 
+GRnnData works similarly to anndata. The goal was to use the .varm/.varp of anndata to store the GRN data associated with a dataset and have a formal way to work with GRNs.
 
-Awesome gene regulatory network enhanced anndata created by @jkobject & remi trimbour
+GRnnData is a subclass of anndata.AnnData, it enforces only that a .varp exists for the anndata
 
-grnndata works similarly to anndata. The goal was to use the .varm of anndata to store the GRN data associated with a dataset and have a formal way to work with GRNs.
+GRnnData also contains multiple helper functions to work with GRNs in scRNAseq like compute_connectivities, get_centrality, compute_cluster, enrichment, metrics, etc. but also accessing the grn with .grn, .targets, .regulators,...
 
-grnndata is a subclass of anndata.AnnData, it enforces only that a .varm exists for the anndata
-
-grnndata also contains multiple helper functions to work with GRNs in scRNAseq
+The package has been designed together with the [scPRINT paper](https://doi.org/10.1101/2024.07.29.605556) and [model](https://github.com/cantinilab/scPRINT), and the GRN benchmarking tool [BenGRN](https://github.com/jkobject/BenGRN)
 
 ## Install it from PyPI
 
 ```bash
 pip install grnndata
 ```
 
+### Install it locally and run the notebooks:
+
+```bash
+git clone https://github.com/cantinilab/GRnnData.git
+pip install -e GRnnData
+```
+
 ## Usage
 
 ```py
-from grnndata import GRNAnnData
+from grnndata import GRNAnnData, read_h5ad
 from grnndata import utils
 
-grn = GRNAnnData(subdata.copy(), grn=grn[1:,1:])
+grn = np.random.rand(10,10)
+adata = anndata.AnnData(X=np.random.rand(10,10))
+
+grn = GRNAnnData(adata, grn=grn)
+
+print(grn) #shows the number of elements
+grn.varp['GRN'] or grn.grn #shows the GRN
+subgrn = grn.get(['gene1', 'gene2']) #only gets some elements from the GRN
+subgrn.targets #shows the target connections
+subgrn.plot() # displays the network
+
+subgrn.write_h5ad('grn.h5ad') #writes it
+read_h5ad('grn.h5ad') #reads it
+
+# or use some utils functions like:
+# compute_connectivities
+# get_centrality
+# compute_cluster
+# enrichment
+# metrics
+# see more in the documentation
+
 utils.some_function(grn)
 ```
 
-grnndata works similarly to anndata. Learn more about usages in the documentation and its notebooks in the [docs](https://cantinilab.github.io/GRnnData/). 
+GRnnData works similarly to anndata. Learn more about usages in the documentation and its notebooks in the [docs](https://cantinilab.github.io/GRnnData/). 
+
+usage examples can be seen in the example notebooks of:
+- [scPRINT](https://www.jkobject.com/scPRINT/notebooks/cancer_usecase/)
+- [BenGRN](https://www.jkobject.com/benGRN/notebooks/bench_omni_genie3/)
 
 ### How do I do if I generate a GRN per cell type?
 
@@ -42,3 +80,5 @@ In this context, we recommend trying to merge them across a similar group of cel
 ## Development
 
 Read the [CONTRIBUTING.md](CONTRIBUTING.md) file.
+
+Awesome gene regulatory network enhanced anndata created by @jkobject
diff --git a/docs/index.md b/docs/index.md
@@ -1,22 +1,73 @@
-# grnndata (putting the grn in anndata)
+# GRnnData
 
-Awesome gene regulatory network enhanced anndata created by jkobject & remi trimbour
+[![codecov](https://codecov.io/gh/cantinilab/GRnnData/branch/main/graph/badge.svg?token=GRnnData_token_here)](https://codecov.io/gh/cantinilab/GRnnData)
+[![CI](https://github.com/cantinilab/GRnnData/actions/workflows/main.yml/badge.svg)](https://github.com/cantinilab/GRnnData/actions/workflows/main.yml)
+[![PyPI version](https://badge.fury.io/py/GRnnData.svg)](https://badge.fury.io/py/benGRN)
+[![Documentation Status](https://readthedocs.org/projects/GRnnData/badge/?version=latest)](https://GRnnData.readthedocs.io/en/latest/?badge=latest)
+[![Downloads](https://pepy.tech/badge/GRnnData)](https://pepy.tech/project/GRnnData)
+[![Downloads](https://pepy.tech/badge/GRnnData/month)](https://pepy.tech/project/GRnnData)
+[![Downloads](https://pepy.tech/badge/GRnnData/week)](https://pepy.tech/project/GRnnData)
+[![GitHub issues](https://img.shields.io/github/issues/cantinilab/GRnnData)](https://img.shields.io/github/issues/cantinilab/GRnnData)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+[![DOI](https://img.shields.io/badge/DOI-10.1101%2F2024.07.29.605556-blue)](https://doi.org/10.1101/2024.07.29.605556)
 
-grnndata works similarly to anndata. The goal was to use the .varm of anndata to store the GRN data associated with a dataset and have a formal way to work with GRNs.
+GRnnData works similarly to anndata. The goal was to use the .varm/.varp of anndata to store the GRN data associated with a dataset and have a formal way to work with GRNs.
 
-grnndata is a subclass of anndata.AnnData, it enforces only that a .varm exists for the anndata
+GRnnData is a subclass of anndata.AnnData, it enforces only that a .varp exists for the anndata
 
-grnndata also contains multiple helper functions to work with GRNs in scRNAseq
+GRnnData also contains multiple helper functions to work with GRNs in scRNAseq like compute_connectivities, get_centrality, compute_cluster, enrichment, metrics, etc. but also accessing the grn with .grn, .targets, .regulators,...
+
+The package has been designed together with the [scPRINT paper](https://doi.org/10.1101/2024.07.29.605556) and [model](https://github.com/cantinilab/scPRINT), and the GRN benchmarking tool [BenGRN](https://github.com/jkobject/BenGRN)
 
 ## Install it from PyPI
 
 ```bash
 pip install grnndata
 ```
 
+### Install it locally and run the notebooks:
+
+```bash
+git clone https://github.com/cantinilab/GRnnData.git
+pip install -e GRnnData
+```
+
 ## Usage
 
-grnndata works similarly to anndata
+```py
+from grnndata import GRNAnnData, read_h5ad
+from grnndata import utils
+
+grn = np.random.rand(10,10)
+adata = anndata.AnnData(X=np.random.rand(10,10))
+
+grn = GRNAnnData(adata, grn=grn)
+
+print(grn) #shows the number of elements
+grn.varp['GRN'] or grn.grn #shows the GRN
+subgrn = grn.get(['gene1', 'gene2']) #only gets some elements from the GRN
+subgrn.targets #shows the target connections
+subgrn.plot() # displays the network
+
+subgrn.write_h5ad('grn.h5ad') #writes it
+read_h5ad('grn.h5ad') #reads it
+
+# or use some utils functions like:
+# compute_connectivities
+# get_centrality
+# compute_cluster
+# enrichment
+# metrics
+# see more in the documentation
+
+utils.some_function(grn)
+```
+
+GRnnData works similarly to anndata. Learn more about usages in the documentation and its notebooks in the [docs](https://cantinilab.github.io/GRnnData/). 
+
+usage examples can be seen in the example notebooks of:
+- [scPRINT](https://www.jkobject.com/scPRINT/notebooks/cancer_usecase/)
+- [BenGRN](https://www.jkobject.com/benGRN/notebooks/bench_omni_genie3/)
 
 ### How do I do if I generate a GRN per cell type?
 
@@ -28,4 +79,6 @@ In this context, we recommend trying to merge them across a similar group of cel
 
 ## Development
 
-Read the [CONTRIBUTING.md](CONTRIBUTING.md) file.
+Read the [CONTRIBUTING.md](../CONTRIBUTING.md) file.
+
+Awesome gene regulatory network enhanced anndata created by @jkobject
diff --git a/docs/notebooks/example.ipynb b/docs/notebooks/example.ipynb
@@ -772,7 +772,7 @@
   },
   "language_info": {
    "name": "python",
-   "version": "3.10.0"
+   "version": "3.10.14"
   }
  },
  "nbformat": 4,