API

Import Harreman as:

import harreman

Datasets

datasets.load_visium_mouse_colon_dataset	Load the mouse colon 10x Visium dataset.
datasets.load_slide_seq_human_lung_dataset	Load the human lung Slide-seq dataset.

Hotspot functions for metabolic zonation

hotspot.load_metabolic_genes	Load the list of metabolic genes for a given species.
hotspot.compute_local_autocorrelation	Computes gene-level spatial autocorrelation statistics using spatial weights and centered gene expression values.
hotspot.compute_local_correlation	Computes pairwise local correlation between selected genes using a spatial weight matrix.
hotspot.create_modules	Perform hierarchical clustering on gene-gene local correlation Z-scores to assign gene modules.
hotspot.calculate_module_scores	Calculate module scores for gene modules across cells.
hotspot.compute_top_scoring_modules	Identify the top-scoring module (or super-module) for each cell.
hotspot.calculate_super_module_scores	Calculate super-module scores for gene super-modules across cells.

Interaction database

preprocessing.extract_interaction_db

Extract the metabolite transporter or ligand-receptor (LR) database from .csv files.

Setting up deconvolution AnnData

preprocessing.setup_deconv_adata

Set up deconvolution AnnData.

Metabolic crosstalk

tools.compute_knn_graph	Computes the spatial proximity graph.
tools.apply_gene_filtering	Applies multi-step gene filtering to an AnnData object.
tools.compute_gene_pairs	Identifies biologically plausible gene pairs involved in ligand-receptor (LR) signaling or metabolite transport based on annotated interaction databases and filtered expression data.
tools.compute_cell_communication	Computes spatially-informed cell-type-agnostic cell-cell communication (CCC) scores and significance across all gene pairs using both parametric and non-parametric statistical tests.
tools.compute_ct_cell_communication	Computes cell type-aware cell-cell communication (CCC) scores by stratifying communication by interacting cell type pairs.
tools.select_significant_interactions	Select significant gene pairs or metabolite-mediated interactions based on FDR/p-value thresholds and (optionally) cell-type–aware tests.
tools.compute_interacting_cell_scores	Compute interacting cell scores for gene pairs and metabolites.
tools.compute_ct_interacting_cell_scores	Compute cell-type–aware interacting cell scores for gene pairs and metabolites.
tools.compute_interaction_module_correlation	Compute correlations between interacting cell scores and module scores.

Visualization

plots.local_correlation_plot	Plot a hierarchical-clustered heatmap of pairwise correlation Z-scores.
plots.average_local_correlation_plot	Plot the average pairwise correlation Z-scores between modules.
plots.module_score_correlation_plot	Plot correlations between module scores across cells.
plots.plot_interacting_cell_scores	Plot spatial maps of interacting cell scores for selected gene pairs or metabolites.
plots.plot_ct_interacting_cell_scores	Plot cell-type–specific interacting cell scores (for gene pairs or metabolites) across spatial coordinates.

Reading/writing functions

read_h5ad	Load an AnnData object from disk and restore Harreman-specific metadata.
write_h5ad	Save an AnnData object to disk with Harreman-compatible preprocessing.