Metadata-Version: 2.4
Name: adataviz
Version: 0.2
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
        to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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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
### to_pseudobulk
```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
```
