Read Visium HD Example Data from GitHub — read

Downloads and loads spatial transcriptomics data from the Visium HD example dataset hosted on a public GitHub repository. This includes spatial coordinates, gene expression counts, deconvolution results, and effective niche estimates.

Usage

read_visiumHD()

Value

A named list with four elements:

coords: A matrix or data frame of spatial coordinates (x and y) for each spot.
niche: A matrix, data frame, or list representing effective niche composition per spot.
deconv: A matrix or data frame of cell type deconvolution proportions per spot.
counts: A gene expression count matrix (genes × spots).

Details

This function requires an internet connection to download data from https://github.com/kaishumason/SpotGLM-Example-Data. The repository must contain the files coords.rds, deconv_matrix.rds, count_matrix_subset.rds, and niche.rds in the visiumHD folder.

Examples

if (FALSE) { # \dontrun{
data_list <- read_visiumHD()
head(data_list$coords)
dim(data_list$counts)
} # }