Basic tutorial

import scanpy as sc
import enrichmap as em

# Load your AnnData object
adata = sc.read_h5ad("PATH/TO/YOUR/DATA.h5ad")

# Define a gene set
gene_set = ["CD3D", "CD3E", "CD8A"]

# Run scoring
em.tl.score(
    adata,
    gene_list=gene_set,
    score_key="T_cell_signature",
    batch_key=None  # Set batch_key if working with multiple slides
)

# Visualise
em.pl.spatial_enrichmap(
    adata=adata,
    score_key="T_cell_signature"
)

Note

EnrichMap currently does not support reading in SpatialData format. However, users can simply convert SpatialData to legacy AnnData to use EnrichMap.

import spatialdata_io as sd
# Read in SpatialData
sdata = sd.visium_hd("PATH_TO_DATA_FOLDER/")
# Convert to AnnData
adata = to_legacy_anndata(
    sdata,
    include_images=True,
    table_name="square_008um",
    coordinate_system="downscaled_hires"
)