summarize_STlist: summarize_STlist: Generates a data frame with summary...

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

summarize_STlist: Generates a data frame with summary statistics

Description

Produces a data frame with counts per gene and counts per ROI/spot/cell

Usage

summarize_STlist(x = NULL)

Arguments

x

an STlist

Details

The function creates a table with counts per gene and counts per region of interest (ROI), spot, or cell in the samples stored in the STlist

Value

a data frame

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[c(1,2)],
                   spotcoords=coord_files[c(1,2)],
                   samples=clin_file) # Only first two samples
summarize_STlist(melanoma)

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