SpaGFT: Graph fourier transformer for representation, analysis, and interpretation of spatially variable genes

Given a gene expression matrix that consists of $n$ spots as well as their spatial coordinates and $n$ genes, SpaGFT can detect spatially variable genes (SVG) and identify tissue modules that are determined by a group of SVGs with similar spatial patterns.

System Requirments

Hardware Requirements

SpaGFT is friendly to hardware. All functions in SpaGFT need the minimum requirements of a CPU with 4 cores and 4G RAM. For large datasets, a large RAM is required to avoid memory overflow.

OS requirements

SpaGFT can run on Windows, Linux, Mac os. The package has been tested on the following systems:

Linux: Ubuntu 20.04
Windows: Windows 10

Python Dependencies

SpaGFT requires python version >= 3.7.


kneed==0.7.0
louvain==0.7.1
matplotlib==3.5.2
networkx==2.8
numba==0.55.1
numpy =1.21.5
pandas==1.4.2
plotnine==0.8.0
scanpy==1.9.1
scikit-learn==1.0.2
scipy==1.8.0
gseapy==0.10.8

Installation Guide

Create a virtual environment

The virtual environment is recommended before installing SpaGFT. Users can install anaconda by following this tutorial. [https://www.anaconda.com/]

If users do not have conda please install Miniconda first:

cd /path/to/software
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Create a separated virtual environment

conda create -n spagft_env python==3.8.0
conda activate spagft_env

If users want to quit this virtual environment, just run conda deactivate

Install `SpaGFT`

Approach 1: install `SpaGFT` by `pip`

Users can install SpaGFT easily in this way by

pip install SpaGFT

Users can also install SpaGFT via Github if there exists any problems.

Approach 2: install `SpaGFT` via Github

Before installing SpaGFT formally, the dependency packages should be installed.

Users can install all dependencies by:

git clone https://github.com/OSU-BMBL/SpaGFT
cd SpaGFT
pip install -r requirements.txt

Next, run

python setup.py install

Note that we recommend jupyter for interactive usage. It can be installed and configured by

conda install jupyter
python -m ipykernel install --user --name=spagft_env --display-name=spagft_env

Usage and Tutorials

The tutorial of SpaGFT could be found here.

Wang-Cankun/SpaGFT