https://github.com/mvinyard/ann_nmf

AnnData wrapper of the ARD-NMF module from SignatureAnalyzer
https://github.com/mvinyard/ann_nmf

anndata nmf single-cell

Last synced: 3 months ago
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AnnData wrapper of the ARD-NMF module from SignatureAnalyzer

• Host: GitHub
• URL: https://github.com/mvinyard/ann_nmf
• Owner: mvinyard
• License: mit
• Created: 2022-02-16T19:48:39.000Z (over 3 years ago)
• Default Branch: main
• Last Pushed: 2022-06-06T04:06:26.000Z (almost 3 years ago)
• Last Synced: 2025-02-28T09:32:04.203Z (3 months ago)
• Topics: anndata, nmf, single-cell
• Language: Jupyter Notebook
• Homepage:
• Size: 239 KB
• Stars: 1
• Watchers: 1
• Forks: 0
• Open Issues: 3
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# ![ann_nmf.logo](docs/imgs/ann_nmf.logo.svg)

[![PyPI pyversions](https://img.shields.io/pypi/pyversions/ann_nmf.svg)](https://pypi.python.org/pypi/ann_nmf/)

[![PyPI version](https://badge.fury.io/py/ann_nmf.svg)](https://badge.fury.io/py/ann_nmf)

[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)

AnnData wrapper of the [**ARD-NMF module**](https://github.com/broadinstitute/SignatureAnalyzer-GPU/blob/master/ARD_NMF.py) from [**SignatureAnalyzer-GPU**](https://github.com/broadinstitute/SignatureAnalyzer-GPU).

## Installation

Install using [pip](https://pypi.org/project/ann-nmf/)

```BASH

pip install ann_nmf

```

Alternatively, install the development version:

```BASH

git clone https://github.com/mvinyard/ann_nmf.git; cd ann_nmf;

pip install -e .

```

## API overview

#### Import libraries and get some data

```python

import ann_nmf

import scanpy as sc

adata = sc.datasets.pbmc3k()

ann_nmf.ut.preprocess_raw_counts(adata)

```

#### Key class:

```python

nmf = ann_nmf.NMF(adata, outdir="nmf_results/pbmc3k") # saves .h5 file

nmf.run(n_runs=10, K0=20, max_iter=2000)

```

#### SignatureAnalyzer visualization:

```python

nmf.cluster()

nmf.signatures()

```



```python

nmf.plot_umap_signatures(adata)

```

![image](https://user-images.githubusercontent.com/47393421/156896803-d835c4e0-9fa5-460a-a194-cfc63af2fa77.png)

```python

ann_nmf.ut.fetch_signature(nmf.nmf_genes, 1)

```



## Conceptual background and foundational work

* ARD-NMF theory [Arxiv](https://arxiv.org/pdf/1111.6085.pdf)

* SignatureAnalyzer ([GitHub](https://github.com/getzlab/getzlab-SignatureAnalyzer))

* SignatureAnalyzer-GPU ([GitHub](https://github.com/broadinstitute/SignatureAnalyzer-GPU))

## Acknowledgements

* Most of the code to wrap SignatureAnalyzer in an AnnData-friendly API was borrowed directly (and shamelessly) from **Shankara Anand** (**[@shankara-a](https://github.com/shankara-a)**) with only slight refactoring for more flexibility with fewer dependencies on install.