Metadata-Version: 2.4
Name: adataviz
Version: 0.3.post0
Summary: A python package to visualize adata
Home-page: https://github.com/DingWB/adataviz
Author: Wubin Ding
Author-email: Wubin Ding <ding.wu.bin.gm@gmail.com>
License: MIT License
        
        Copyright (c) 2026 Wubin Ding
        
        Permission is hereby granted, free of charge, to any person obtaining a copy
        of this software and associated documentation files (the "Software"), to deal
        in the Software without restriction, including without limitation the rights
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        The above copyright notice and this permission notice shall be included in all
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        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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Project-URL: Homepage, https://github.com/DingWB/adataviz
Project-URL: repository, https://github.com/DingWB/adataviz
Project-URL: Bug Tracker, https://github.com/DingWB/adataviz/issues
Project-URL: documentation, https://dingwb.github.io/adataviz
Keywords: adata,visualization
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: MIT License
Classifier: Operating System :: OS Independent
Requires-Python: >=3.0
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: matplotlib
Requires-Dist: numpy
Requires-Dist: pandas>=1.3.5
Requires-Dist: scipy
Requires-Dist: loguru
Requires-Dist: anndata
Requires-Dist: fire
Requires-Dist: scanpy
Requires-Dist: PyComplexHeatmap
Requires-Dist: seaborn
Requires-Dist: adjustText
Requires-Dist: plotly
Requires-Dist: ipywidgets
Dynamic: author
Dynamic: home-page
Dynamic: license-file

# adataviz
Functions and tools to visualize adata

## **Installation**
----------------------
1. **Install using pip**:
```shell
pip install adataviz

#upgrade from older version
pip install --upgrade adataviz
```

2. **Install the developmental version directly from github**:
```shell
pip install git+https://github.com/DingWB/adataviz
# reinstall
pip uninstall -y adataviz && pip install git+https://github.com/DingWB/adataviz

```
OR
```shell
git clone https://github.com/DingWB/adataviz
cd adataviz
python setup.py install
```

## Command Line Tools
### Aggregrate single-cell RNA data to pseudobulk adata
```shell
# merge single cells raw counts to psuedobulk (sum up raw counts) and run normalization (logCPM or logTPM)
adataviz tool scrna2pseudobulk  HMBA.Group.downsample_1500.h5ad --groupby="Subclass" --downsample=2000 --use_raw=True --n_jobs 16 --normalization CPM -s ~/Projects/BICAN/adata/HMBA_v2/Pseudobulk.Subclass.h5ad

# stat pseudobulk: calculate min,q25, q50, q75, max, mean and std
adataviz tool stat_pseudobulk  HMBA.Group.downsample_1500.h5ad --groupby="Subclass" --downsample=2000 --use_raw=False -m RNA --n_jobs 16 -s ~/Projects/BICAN/adata/HMBA_v2/Pseudobulk.Subclass.stats.h5ad
```
