pseudobulk_samples: pseudobulk_samples: Aggregates counts into "pseudo bulk"...

In FridleyLab/spatialGE: Visualization and Analysis of Spatial Heterogeneity in Spatially-Resolved Gene Expression

pseudobulk_samples: Aggregates counts into "pseudo bulk" samples

Description

Aggregates spot/cell counts into "pseudo bulk" samples for data exploration

Usage

pseudobulk_samples(x = NULL, max_var_genes = 5000, calc_umap = F)

Arguments

x	an STlist.
max_var_genes	number of most variable genes (standard deviation) to use in pseudobulk analysis
calc_umap	logical, whether to calculate UMAP embeddings in addition to PCs

Details

This function takes an STlist and aggregates the spot/cell counts into "pseudo bulk" counts by summing all counts from all cell/spots for each gene. Then performs Principal Component Analysis (PCA) to explore non-spatial sample-to-sample variation

Value

an STlist with appended pseudobulk counts and PCA coordinates

Examples

# Using included melanoma example (Thrane et al.)
# Download example data set from spatialGE_Data
thrane_tmp = tempdir()
unlink(thrane_tmp, recursive=TRUE)
dir.create(thrane_tmp)
lk='https://github.com/FridleyLab/spatialGE_Data/raw/refs/heads/main/melanoma_thrane.zip?download='
download.file(lk, destfile=paste0(thrane_tmp, '/', 'melanoma_thrane.zip'), mode='wb')
zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
unzip(zipfile=zip_tmp, exdir=thrane_tmp)
# Generate the file paths to be passed to the STlist function
count_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                          full.names=TRUE, pattern='counts')
coord_files <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                          full.names=TRUE, pattern='mapping')
clin_file <- list.files(paste0(thrane_tmp, '/melanoma_thrane'),
                        full.names=TRUE, pattern='clinical')
# Create STlist
library('spatialGE')
melanoma <- STlist(rnacounts=count_files,
                   spotcoords=coord_files,
                   samples=clin_file, cores=2)
melanoma <- pseudobulk_samples(melanoma)
pseudobulk_dim_plot(melanoma)

FridleyLab/spatialGE documentation built on April 14, 2025, 9:37 a.m.