Package 'stIHC'

Title: Spatial Transcriptomics Iterative Hierarchical Clustering
Description: Spatial transcriptomics iterative hierarchical clustering ('stIHC'), is a method for identifying spatial gene co-expression modules, defined as groups of genes with shared spatial expression patterns. The method is applicable across spatial transcriptomics technologies with differing spatial resolution, and provides a framework for investigating the spatial organisation of gene expression in tissues. For further details, see Higgins C., Li J.J., Carey M. <doi:10.1002/qub2.70011>.
Authors: Catherine Higgins [aut, cre], Jingyi Jessica Li [aut], Michelle Carey [aut]
Maintainer: Catherine Higgins <[email protected]>
License: MIT + file LICENSE
Version: 0.1.0
Built: 2026-05-12 08:27:14 UTC
Source: https://github.com/cran/stIHC

Help Index

Spatial Transcriptomics Iterative Hierarchical Clustering

Description

Spatial Transcriptomics Iterative Hierarchical Clustering

Usage

stIHC(data)

Arguments

data

data frame with columns x, y for spatial coordinates and subsequent columns containing observations.

Value

A list with elements:

label

Vector of cluster labels.
mean_clusters_mat

Matrix of cluster means.
clusters

List of matrices, each matrix contains the observations belonging to that cluster.

Examples

## Load example data within the package
rds_path <- system.file("extdata", "spatial_data.rds", package = "stIHC")
example_data <- readRDS(rds_path)

## Run stIHC
stihc = stIHC(example_data)

## Inspect cluster assignments
table(stihc$label)