tests/testthat/test_dataImports.R

In drieslab/Giotto_site_suite: Spatial Single-Cell Transcriptomics Toolbox

# python_path = NULL
# if(is.null(python_path)) {
#   installGiottoEnvironment()
# }

if(!require(remotes)){
  install.packages('R.utils', repos = 'http://cran.us.r-project.org')
}

if(!require(remotes)){
  install.packages('remotes', repos = 'http://cran.us.r-project.org')
}

if(!require(GiottoData)){
  library(remotes)
  install_github('drieslab/GiottoData')
}

### TESTS FOR DATA IMPORT FUNCTIONS
# ------------------------------------

test_that("Expression matrix is read correctly", {
  
  # getSpatialDataset
  GiottoData::getSpatialDataset(dataset = "scRNA_mouse_brain", directory = paste0(getwd(), "/testdata/"))
  
  # readExprMatrix
  expr_mat <- readExprMatrix(paste0(getwd(), "/testdata/brain_sc_expression_matrix.txt.gz"))

  expect_s4_class(expr_mat, "dgCMatrix")
  expect_equal(expr_mat@Dim, c(27998, 8039))

  # check a few genes
  expect_equal(expr_mat@Dimnames[[1]][20], "Sgcz")
  expect_equal(expr_mat@Dimnames[[1]][50], 'Zfp804a')
})

# get10Xmatrix_h5
# TODO

# stitchFieldCoordinates
# TODO

# stitchTileCoordinates
# TODO

# -----------------------------
# remove files after testing
if (file.exists("./testdata/brain_sc_expression_matrix.txt.gz")) {
  unlink("./testdata/brain_sc_expression_matrix.txt.gz")
}

if (file.exists("./testdata/brain_sc_metadata.csv")) {
  unlink("./testdata/brain_sc_metadata.csv")
}