Create test-summarize-by-patient.R

tests/testthat/test-summarize-by-patient.R

@@ -0,0 +1,152 @@
+
+# Test Binary Matrix Arguments -----------------------------------------------------------
+
+# General tests ---
+# test_that("test simplify marix with no errors", {
+#
+#   cna <- pivot_cna_longer(gnomeR::cna)
+#   samples <- as.character(unique(gnomeR::mut$Tumor_Sample_Barcode))[1:50]
+#   gen_dat <- create_gene_binary(samples = samples,
+#                                 mutation = gnomeR::mut,
+#                                 fusion = gnomeR::fusion,
+#                                 cna = cna)
+#
+#   gen_dat2 <- gnomeR::summarize_by_gene(gen_dat)
+#
+#   tp53_1 <- gen_dat %>% select(contains("TP53"))
+#   tp53_1 <- (tp53_1$TP53== 1 |tp53_1$TP53.Del== 1)%>% sum()
+#
+#   tp53_2 <- gen_dat2$TP53 %>% sum()
+#   expect_equal(tp53_1, tp53_2)
+#
+#   expect_equal(length(table(gen_dat2$TP53)), 2)
+# })
+
+test_that("test simplify marix needs a data frame", {
+
+  expect_error(summarize_by_gene(gene_binary = c(1:10)))
+
+})
+
+test_that("test simplify matrix needs a data frame", {
+
+  samples <- as.character(unique(gnomeR::mutations$sampleId))[1:50]
+  gen_dat <- create_gene_binary(samples = samples,
+                                mutation = gnomeR::mutations,
+                                fusion = gnomeR::sv)
+
+  expect_no_error(gen_dat2 <- gnomeR::summarize_by_gene(gen_dat))
+
+
+})
+
+
+test_that("test that genes are properly summarized", {
+  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId, gnomeR::cna$sampleId,
+                                    gnomeR::sv$sampleId))
+
+
+  expect_message(bin_impact <-  create_gene_binary(samples=samples,
+                                                   mutation = gnomeR::mutations,
+                                                   cna = gnomeR::cna,
+                                                   fusion = gnomeR::sv,
+                                                   specify_panel = "impact")%>%
+                   dplyr::select(c(sample_id, starts_with("ARI"), starts_with("MAPK1"), starts_with("ERG"))))
+
+
+  sum_impact <- summarize_by_gene(bin_impact)%>%
+    dplyr::mutate(across(!sample_id, as.numeric))
+
+
+  bin_impact_test <- bin_impact %>%
+    tidyr::pivot_longer(!sample_id)%>%
+    mutate(name = str_remove(name, ".Amp|.Del|.fus"))%>%
+    tidyr::pivot_wider(names_from = name, values_from = value, values_fn = function (x) sum(x))%>%
+    mutate(across(!sample_id, ~ifelse(. > 0, 1, 0)))%>%
+    relocate(colnames(sum_impact))
+
+  expect_equal(sum_impact, bin_impact_test)
+
+
+})
+
+
+test_that("test what happens to columns with all NA", {
+
+  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId, gnomeR::cna$sampleId,
+                                    gnomeR::sv$sampleId))
+
+
+  bin_impact <-  create_gene_binary(samples=samples,
+                                    mutation = gnomeR::mutations,
+                                    cna = gnomeR::cna,
+                                    fusion = gnomeR::sv,
+                                    specify_panel = "impact") %>%
+    select(c(sample_id, starts_with("AR"), starts_with("PLCG2"), starts_with("PPM1D")))
+
+
+  sum_impact <- summarize_by_gene(bin_impact)%>%
+    mutate(across(!sample_id, as.numeric))
+
+
+  bin_impact_test <- bin_impact %>%
+    tidyr::pivot_longer(!sample_id)%>%
+    mutate(name = str_remove(name, ".Amp|.Del|.fus"))%>%
+    tidyr::pivot_wider(names_from = name, values_from = value, values_fn = function (x) sum(x))%>%
+    mutate(across(!sample_id, ~ifelse(. > 0, 1, 0)))%>%
+    relocate(colnames(sum_impact))%>%
+    mutate_if(~ all(is.na(.)), ~as.numeric(NA_integer_))
+
+  expect_equal(sum_impact, bin_impact_test)
+
+  expect_equal(ncol(as.data.frame(
+    sum_impact[,sapply(sum_impact, function(x) all(is.na(x)))])), 1)
+
+})
+
+
+test_that("other vars are retained", {
+  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId,
+                                    gnomeR::cna$sampleId,
+                                    gnomeR::sv$sampleId))
+
+
+  bin_impact <- create_gene_binary(samples = samples,
+                                   mutation = gnomeR::mutations,
+                                   cna = gnomeR::cna,
+                                   fusion = gnomeR::sv,
+                                   specify_panel = "impact") %>%
+    select(c(sample_id, starts_with("AR"), starts_with("PLCG2"), starts_with("PPM1D")))
+
+  set.seed(20230828)
+
+  bin_impact$random_color = sample(c("blue", "red", "yellow"),
+                                   size = 50, replace = TRUE)
+
+  expect_true("random_color" %in% names(bin_impact))
+  sum_impact <- summarize_by_gene(bin_impact,
+                                  other_vars = "random_color")
+
+  expect_true("random_color" %in% names(sum_impact))
+  expect_true("blue" %in% sum_impact$random_color)
+})
+
+
+test_that("no warning message thrown when only 1 alt type", {
+
+  samples <- gnomeR::mutations$sampleId
+  bin.mut <- create_gene_binary(
+    samples = samples, mutation = gnomeR::mutations,
+    mut_type = "omit_germline", snp_only = FALSE,
+    include_silent = FALSE
+  )
+
+  expect_no_warning(summarize_by_gene(bin.mut))
+
+
+
+})
+
+
+
+