Contents

Getting Started!

To install SpatialTis, please see the Installation section. It’s recommended to start a new virtual environment before installing the SpatialTis.

Prerequisites

Must learn:

Optional:

  • numpy: For array operation

  • pandas: For table operation

  • scanpy: Used for cell type calling and scRNA-seq related analysis

Basic Usage

Before any analysis using SpatialTis, it’s necessary to set up some global config, so that you don’t need to specific them every time:

from spatialtis import CONFIG

CONFIG.EXP_OBS = ['Patient', 'Sample', 'ROI']
CONFIG.ROI_KEY = 'ROI'
CONFIG.CELL_TYPE_KEY = 'cell_type'
CONFIG.CENTROID_KEY = 'centroid'
CONFIG.MARKERS_KEY = 'markers'

There are an analysis module and a visualization module plotting in SpatialTis:

import spatialtis as st
import spatialtis.plotting as sp

First load the data:

from anndata import read_h5ad
data = read_h5ad('sample.h5ad')

Normally an analysis function comes with a visualization function, they share the same name but registered in different modules. DON’T import these functions individually, it will cause conflicts

Call an analysis function for cell_components:

st.cell_components(data)

Call visualization function for cell_components:

sp.cell_components(data)

Now that you’ve learn some basic of SpatialTis, feel free to play around. If you want to know more about analysis and visualization with SpatialTis, check the Tutorial.

Welcome to SpatialTis’s documentation! Example