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

In 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='
tryCatch({ # In case data is not available from network
  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) # Only first two samples
  summarize_STlist(melanoma)
}, error = function(e) {
  message("Could not run example. Are you connected to the internet?.")
  return(NULL)
})

spatialGE documentation built on June 8, 2025, 11:10 a.m.