tests/testthat/test-tests.R

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

##
# Unit tests via testthat
#

# Create STlist from Thrane et al. data
thrane_tmp = tempdir()
unlink(thrane_tmp, recursive=TRUE)
dir.create(thrane_tmp)
zip_tmp = tryCatch({ # In case data is not available from network
  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', quiet=TRUE)
  zip_tmp = list.files(thrane_tmp, pattern='melanoma_thrane.zip$', full.names=TRUE)
}, error = function(e) {
  zip_tmp = ''
  message("Could not download data.")
  return(zip_tmp)
})

if(file.exists(zip_tmp)){
  unzip(zipfile=zip_tmp, exdir=thrane_tmp)
  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')
  # library('spatialGE')
  melanoma = STlist(rnacounts=count_files[c(1,2)], spotcoords=coord_files[c(1,2)], samples=clin_file) # Only first two samples

  # Test that resulting STlist is an S4 object
  testthat::test_that("Data input checks output single character string", {
    testthat::expect_s4_class(melanoma, 'STlist')
  })
}