EnrichMap is a lightweight tool designed to compute and visualise enrichment scores of a given gene set or signature in spatial transcriptomics datasets across different platforms. It offers flexible scoring, batch correction, spatial smoothing and visual outputs for intuitive exploration of biological signatures.
- Fast computation of enrichment scores
- Support for batch correction and spatial covariates
- Built-in spatial smoothing
- Visualisation tools for intuitive mapping
- Easy integration with AnnData (.h5ad) objects
A conda environment is strongly recommended with python ≥ 3.10.
conda create -n enrichmap_env python=3.11
conda activate enrichmap_envThen, install enrichmap via pip.
pip install enrichmapor directly from GitHub:
pip install git+https://github.com/secrierlab/enrichmap.gitimportscanpyasscimportenrichmapasem# Load your AnnData objectadata=sc.read_h5ad("PATH/TO/YOUR/DATA.h5ad")
# Define a gene setgene_set= ["CD3D", "CD3E", "CD8A"]
# Run scoringem.tl.score(
adata=adata,
gene_set=gene_set,
score_key="T_cell_signature",
smoothing=True, # by default,correct_spatial_covariates=True, # by defaultbatch_key=None# Set batch_key if working with multiple slides
)
# Visualiseem.pl.spatial_enrichmap(
adata=adata,
score_key="T_cell_signature_score"
)Important note: EnrichMap currently does not support reading in
SpatialDataformat. However, users can simply convertSpatialDatato legacyAnnDatato use EnrichMap.
importspatialdata_ioassd# read in SpatialDatasdata=sd.visium_hd("PATH_TO_DATA_FOLDER/")
# convert to AnnDataadata=to_legacy_anndata(sdata, include_images=True, table_name="square_008um", coordinate_system="downscaled_hires")Comprehensive documentation is available at: https://enrichmap.readthedocs.io/en/latest
If you have ideas for new features or spot a bug, please open an issue or submit a pull request.
This project is licensed under the GNU GENERAL PUBLIC LICENSE.
Celik C & Secrier M (2025). EnrichMap: Spatially-informed enrichment analysis for functional interpretation of spatial transcriptomics. biorxiv.com
This code is free and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY. See the GNU General Public License for more details.