test_that("Annotation options", {


   gimap_dataset <- get_example_data("gimap") %>%
     gimap_filter() %>%
     gimap_annotate(cell_line = "HELA")

   # We should see these columns
   testthat::expect_true(all(c("norm_ctrl_flag",
                               "log2_tpm_gene1", "log2_tpm_gene2",
                               "log2_cn_gene1", "log2_cn_gene2",
                               "gene1_expressed_flag", "gene2_expressed_flag") %in%
                               colnames(gimap_dataset$annotation)))

   # It should warn you if you try to say FALSE for cell line_annotate but
   # don't provide a custom_tpm or use normalize_by_unexpressed = FALSE
   testthat::expect_error(
     gimap_dataset <- get_example_data("gimap") %>%
       gimap_filter() %>%
       gimap_annotate(cell_line_annotate = FALSE) %>%
       gimap_normalize(timepoints = "day"))

   gimap_dataset <- get_example_data("gimap") %>%
     gimap_filter() %>%
     gimap_annotate(cell_line_annotate = FALSE) %>%
     gimap_normalize(timepoints = "day",
                     normalize_by_unexpressed = FALSE)

   # We should see these columns
   testthat::expect_true(all(c("lfc", "crispr_score", "norm_ctrl_flag") %in%
                               colnames(gimap_dataset$normalized_log_fc)))

   ## Try out using custom TPM data
   custom_tpm <- vroom::vroom(file.path(
     system.file("extdata", package = "gimap"),
     "CCLE_expression.csv"),
                       show_col_types = FALSE,
                       col_select = c("genes", "ACH-001086")
   ) %>%
     dplyr::rename(log2_tpm = `ACH-001086`)

   gimap_dataset <- get_example_data("gimap") %>%
     gimap_filter() %>%
     gimap_annotate(custom_tpm = custom_tpm,
                    cell_line = "HELA")

   gimap_dataset <- gimap_dataset %>%
     gimap_normalize(timepoints = "day",
                     normalize_by_unexpressed = FALSE,
                     overwrite = TRUE)

   # We should see these columns
   testthat::expect_true(all(c("lfc", "crispr_score", "norm_ctrl_flag") %in%
                               colnames(gimap_dataset$normalized_log_fc)))
})