Update test-summarize-by-patient.R

Author: jalavery

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

@@ -11,7 +11,7 @@
 #                                 fusion = gnomeR::fusion,
 #                                 cna = cna)
 #
-#   gen_dat2 <- gnomeR::summarize_by_gene(gen_dat)
+#   gen_dat2 <- gnomeR::summarize_by_patient(gen_dat)
 #
 #   tp53_1 <- gen_dat %>% select(contains("TP53"))
 #   tp53_1 <- (tp53_1$TP53== 1 |tp53_1$TP53.Del== 1)%>% sum()
@@ -24,7 +24,7 @@
 
 test_that("test simplify marix needs a data frame", {
 
-  expect_error(summarize_by_gene(gene_binary = c(1:10)))
+  expect_error(summarize_by_patient(gene_binary = c(1:10)))
 
 })
 
@@ -35,11 +35,49 @@ test_that("test simplify matrix needs a data frame", {
                                 mutation = gnomeR::mutations,
                                 fusion = gnomeR::sv)
 
-  expect_no_error(gen_dat2 <- gnomeR::summarize_by_gene(gen_dat))
+  expect_no_error(gen_dat2 <- gnomeR::summarize_by_patient(gen_dat))
 
 
 })
 
+test_that("test output matches summarize_by_gene if only 1 sample per patient", {
+
+  # restrict to 1 sample/patient
+  samples <- gnomeR::mutations %>%
+    mutate(patient_id = gnomeR::extract_patient_id(sampleId)) %>%
+    distinct(patient_id, .keep_all = TRUE) %>%
+    pull(sampleId)
+
+  gen_dat <- create_gene_binary(samples = samples,
+                                mutation = gnomeR::mutations,
+                                fusion = gnomeR::sv)
+
+  expect_equal(gnomeR::summarize_by_gene(gen_dat) %>% select(-sample_id),
+               gnomeR::summarize_by_patient(gen_dat) %>% select(-patient_id))
+
+
+})
+
+test_that("test that output is only 1 row/patient", {
+
+  # restrict to 1 sample/patient
+  # bind gnomeR::mutations to ensure there are duplicates
+  samples <- bind_rows(gnomeR::mutations,
+                       gnomeR::mutations) %>%
+    mutate(patient_id = gnomeR::extract_patient_id(sampleId)) %>%
+    pull(sampleId)
+
+  gen_dat <- create_gene_binary(samples = samples,
+                                mutation = gnomeR::mutations,
+                                fusion = gnomeR::sv)
+
+  n_rec_pt <- gnomeR::summarize_by_patient(gen_dat) %>%
+    count(patient_id, name = "n_rec_pt") %>%
+    distinct(n_rec_pt) %>%
+    pull(n_rec_pt)
+
+  expect_equal(n_rec_pt, n_rec_pt)
+})
 
 test_that("test that genes are properly summarized", {
   samples <- Reduce(intersect, list(gnomeR::mutations$sampleId, gnomeR::cna$sampleId,
@@ -50,24 +88,49 @@ test_that("test that genes are properly summarized", {
                                                    mutation = gnomeR::mutations,
                                                    cna = gnomeR::cna,
                                                    fusion = gnomeR::sv,
-                                                   specify_panel = "impact")%>%
+                                                   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))
+  sum_impact <- summarize_by_patient(bin_impact) %>%
+    dplyr::mutate(across(!patient_id, as.numeric)) %>%
+    arrange(patient_id)
 
 
   bin_impact_test <- bin_impact %>%
-    tidyr::pivot_longer(!sample_id)%>%
+    mutate(patient_id = gnomeR::extract_patient_id(sample_id)) %>%
+    select(-sample_id) %>%
+    tidyr::pivot_longer(cols = c(everything(), -patient_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))
+    tidyr::pivot_wider(names_from = name, values_from = value, values_fn = function (x) sum(x)) %>%
+    mutate(across(.cols = c(-patient_id),
+                  ~ifelse(. > 0, 1, 0))) %>%
+    mutate_if(~ all(is.na(.)), ~as.numeric(NA_integer_))  %>%
+    relocate(colnames(sum_impact)) %>%
+    arrange(patient_id)
 
   expect_equal(sum_impact, bin_impact_test)
+})
+
+test_that("test alteration hierarchy", {
+  # alteration if alteration on any sample
+  # no alteration if no alteration on all samples (no NAs)
+  # else NA
 
+  # dummy binary matrix with comparisons of interest
+  bin_impact_dummy <- tribble(~sample_id, ~ALK, ~EGFR, ~KRAS, ~TP53, ~KMT2D, ~SMARCA4,
+                              paste0(gnomeR::mutations$patientId[1], "-T01", "-IM5"), 1, 0, 1, 1, 0, NA_integer_,
+                              paste0(gnomeR::mutations$patientId[1], "-T01", "-IM5"), 1, 0, 0, NA_integer_, NA_integer_, NA_integer_)
 
+  sum_impact <- summarize_by_patient(bin_impact_dummy) %>%
+    dplyr::mutate(across(!patient_id, as.numeric)) %>%
+    arrange(patient_id)
+
+  bin_impact_expected <- tribble(~patient_id, ~ALK, ~EGFR, ~KRAS, ~TP53, ~KMT2D, ~SMARCA4,
+                                 gnomeR::mutations$patientId[1], 1, 0, 1, 1, NA_integer_, NA_integer_) %>%
+    mutate(across(-patient_id, as.numeric))
+
+  expect_equal(sum_impact, bin_impact_expected)
 })
 
 
@@ -85,17 +148,22 @@ test_that("test what happens to columns with all NA", {
     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))
+  sum_impact <- summarize_by_patient(bin_impact)%>%
+    mutate(across(!patient_id, as.numeric)) %>%
+    arrange(patient_id)
 
 
   bin_impact_test <- bin_impact %>%
-    tidyr::pivot_longer(!sample_id)%>%
+    mutate(patient_id = gnomeR::extract_patient_id(sample_id)) %>%
+    select(-sample_id) %>%
+    tidyr::pivot_longer(cols = c(everything(), -patient_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_))
+    tidyr::pivot_wider(names_from = name, values_from = value, values_fn = function (x) sum(x)) %>%
+    mutate(across(.cols = c(-patient_id),
+                  ~ifelse(. > 0, 1, 0))) %>%
+    mutate_if(~ all(is.na(.)), ~as.numeric(NA_integer_))  %>%
+    relocate(colnames(sum_impact)) %>%
+    arrange(patient_id)
 
   expect_equal(sum_impact, bin_impact_test)
 
@@ -106,10 +174,11 @@ test_that("test what happens to columns with all NA", {
 
 
 test_that("other vars are retained", {
-  samples <- Reduce(intersect, list(gnomeR::mutations$sampleId,
-                                    gnomeR::cna$sampleId,
-                                    gnomeR::sv$sampleId))
-
+  samples <- gnomeR::mutations %>%
+    mutate(patient_id = gnomeR::extract_patient_id(sampleId)) %>%
+    head(50) %>%
+    pull(sampleId) %>%
+    unique()
 
   bin_impact <- create_gene_binary(samples = samples,
                                    mutation = gnomeR::mutations,
@@ -121,11 +190,11 @@ test_that("other vars are retained", {
   set.seed(20230828)
 
   bin_impact$random_color = sample(c("blue", "red", "yellow"),
-                                   size = 50, replace = TRUE)
+                                   size = length(samples), replace = TRUE)
 
   expect_true("random_color" %in% names(bin_impact))
-  sum_impact <- summarize_by_gene(bin_impact,
-                                  other_vars = "random_color")
+  sum_impact <- summarize_by_patient(bin_impact,
+                                     other_vars = "random_color")
 
   expect_true("random_color" %in% names(sum_impact))
   expect_true("blue" %in% sum_impact$random_color)
@@ -141,12 +210,5 @@ test_that("no warning message thrown when only 1 alt type", {
     include_silent = FALSE
   )
 
-  expect_no_warning(summarize_by_gene(bin.mut))
-
-
-
+  expect_no_warning(summarize_by_patient(bin.mut))
 })
-
-
-
-