SpatialDM 0.0.2

SpatialDM: Spatial co-expression Detected by bivariate Moran

About

Installation

SpatialDM is available through PyPI. To install, type the following command line and add -U for updates:

pip install -U spatialdm

Alternatively, you can install from this GitHub repository for latest (often development) version by the following command line:

pip install -U git+https://github.com/leeyoyohku/SpatialDM

Installation time: < 1 min

Quick example

Using the build-in melanoma dataset as an example, the following Python script will compute the p-value indicating whether a certain Ligand-Receptor is spatially co-expressed.

import spatialdm as sdm
adata = sdm.datasets.melanoma()
my_sample = sdm.SpatialDM(X=adata.X, spatialcoord=adata.obsm['spatial'])
my_sample.extract_lr(species='human', min_cell=3)
my_sample.weight_matrix(l=1.2, cutoff=0.2, single_cell=False)
my_sample.spatialdm_global(1000, select_num=None, method='permutation')
sdm.pl.volcano(my_sample)

Detailed Manual

The full manual is at https://spatialdm.readthedocs.io

References

A BioRxiv preprint will be online soon.