Nothing
context("running findCells")
test_that("findCells accurately estimates cell type proportions on the ABA data with combined data", {
expect_identical(colnames(aba_marker_expression), aba_pheno_data$id, "Test data sample IDs match")
ct_res = brainCells(aba_marker_expression, nMarker = 50, species = "combined")
cor_mic = cor.test(ct_res[, "mic"], as.numeric(aba_pheno_data$ihc_iba1_ffpe), method = "spearman")
cor_ast = cor.test(ct_res[, "ast"], as.numeric(aba_pheno_data$ihc_gfap_ffpe), method = "spearman")
expect_equal(as.numeric(round(cor_mic$estimate, 2)), 0.33, info = "Microglia proportion estimation works")
expect_equal(as.numeric(round(cor_ast$estimate, 2)), 0.48, info = "Astrocyte proportion estimation works")
ct_res_marker_df = findCells(aba_marker_expression, markers = markers_df_brain, nMarker = 50)
expect_identical(ct_res, ct_res_marker_df, "alternative interface to findCells works the same")
})
test_that("findCells accurately estimates cell type proportions on the ABA data with human data and without scaling", {
ct_res = brainCells(aba_marker_expression, nMarker = 50, species = "human", scale = FALSE)
cor_mic = cor.test(ct_res[, "mic"], as.numeric(aba_pheno_data$ihc_iba1_ffpe), method = "spearman")
cor_ast = cor.test(ct_res[, "ast"], as.numeric(aba_pheno_data$ihc_gfap_ffpe), method = "spearman")
expect_equal(as.numeric(round(cor_mic$estimate, 2)), 0.33, info = "Microglia proportion estimation works")
expect_equal(as.numeric(round(cor_ast$estimate, 2)), 0.46, info = "Astrocyte proportion estimation works")
})
test_that("findCells accurately estimates cell type proportions on the ABA data with fewer markers and using PCA", {
ct_res = brainCells(aba_marker_expression, nMarker = 10, species = "combined", method = "PCA")
cor_mic = cor.test(ct_res[, "mic"], as.numeric(aba_pheno_data$ihc_iba1_ffpe), method = "spearman")
cor_ast = cor.test(ct_res[, "ast"], as.numeric(aba_pheno_data$ihc_gfap_ffpe), method = "spearman")
expect_equal(as.numeric(round(cor_mic$estimate, 2)), 0.27, info = "Microglia proportion estimation works")
expect_equal(as.numeric(round(cor_ast$estimate, 2)), 0.48, info = "Astrocyte proportion estimation works")
})
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