API Reference#

Main scoring function#

Compute spatially smoothed and spatially corrected gene set enrichment scores for one or more gene signatures.

These functions are used by the score function.

`enrichmap.tl.infer_gene_weights`	Infer gene weights based on the coefficient of variation (CV) of gene expression.
`enrichmap.tl.build_signed_weights`	Build a signed gene weight dictionary from upregulated and downregulated gene lists.

Visualise spatial enrichment maps for given signatures using spatial scatter plots.

Functionalities to assess the smoothness of scores or input gene signature.

`enrichmap.pl.spatial_metrics`	Compute and visualise spatial metrics for different scoring methods in a given dataset.
`enrichmap.pl.compare_morans_i`	Compare spatial autocorrelation of EnrichMap scores across patients using permutation-standardised Moran's I.
`enrichmap.pl.compare_wasserstein`	Pairwise Wasserstein (earth mover's) distance between patients based on spatially embedded EnrichMap scores.
`enrichmap.pl.compare_variograms`	Fit empirical semivariograms to EnrichMap scores per patient and extract structural parameters for cross-patient comparison of spatial organisation.
`enrichmap.pl.variogram`	Compute empirical variograms to assess spatial dependence for any score key.
`enrichmap.pl.variogram_all`	Compute and plot empirical variograms for multiple score keys on the same plot.
`enrichmap.pl.morans_correlogram`	Plot Moran scatterplots (spatial correlograms) for one or multiple spatial libraries.
`enrichmap.pl.cross_moran_scatter`	Plot cross-Moran scatterplots: score_x vs spatial lag of score_y, per library or globally.

Plot a heatmap of correlations between gene set scores in adata.obs.

`enrichmap.pl.gene_contributions_heatmap`	Spatial gene contribution heatmap with expression scaling and spatial ordering.
`enrichmap.pl.gene_contributions_pca`	Visualise gene contributions to a spatial gene signature using PCA-reduced scatter plot.