Metadata-Version: 2.1
Name: RidgeSpace
Version: 0.1.6
Summary: Unravelling three-dimensionally dynamics of spatial multi-modal data
Home-page: http://pypi.python.org/pypi/RidgeSpace/
Author: Ruiqiao He
Author-email: ruiqiaohe@gmail.com
License: GPL
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Requires-Python: >=3.7.1
Description-Content-Type: text/markdown
Requires-Dist: matplotlib (>=3.5.0)
Requires-Dist: numpy
Requires-Dist: pandas
Requires-Dist: scipy

## Unravelling three-dimensionally dynamics of spatial multi-modal data with RidgeSpace

You can freely use RidgeSpace for illustrating, comparing, and tracking the spatial dynamics of molecular signals.

<p align="center">
  <img src='./docs/RidgeSpace.png'>
</p>
<p align="center">
  Overview of RidgeSpace.
</p>

### Prerequisites

    "matplotlib", "numpy", "pandas", "scipy"

### Installation

I suggest that you can freely install RidgeSpace with pip. 

```bash
pip install RidgeSpace
```

You can also use a separate conda environment for installing RidgeSpace.

```bash
conda create -y -n RidgeSpace_env python=3.7
source activate RidgeSpace_env
pip install RidgeSpace
```

### Basic Examples

<p align="center">
  <img src='./docs/Examples.png'>
</p>
<p align="center">
  Examples of RidgeSpace.
</p>

Test data and code for RidgeSpace provided in the "tests" folder.

Single-gene spatial depiction:
```bash
RidgeSpace.pl_single(adata, plot_name = 'Mbp', obs_cluster='Clusters', elev=40, view=160))
```

Multi-modal spatial comparison:
```bash
RidgeSpace.pl_multipleOUT(adata, plot_nameA = 'Tnnt1', plot_nameB = 'Tnnt2', obs_cluster='Clusters', elev=20, view=160, plot_HE_bg=True)
```

Pseudotime spatial trajectory representation:
```bash
RidgeSpace.pl_trajectory(adata, plot_name = 'Pseudotime', obs_cluster='Clusters', elev=45, view=165, HE_z=10)
```

Further tutorials please refer to  https://RidgeSpace.readthedocs.io/.


