add tests scale and order_labels

R/treediff.R

@@ -20,9 +20,9 @@
 #' @param replicates A numeric vector of length 2 with the number of replicates
 #' for each condition.
 #' @param scale Logical. If \code{TRUE}, the trees are all rescaled to have a
-#' minimum height equal to 0 and a maximum height equal to 1. Default to 
+#' minimum height equal to 0 and a maximum height equal to 1. Default to
 #' \code{FALSE}.
-#' @param order_labels Logical. If \code{TRUE}, align leaves ordering in all 
+#' @param order_labels Logical. If \code{TRUE}, align leaves ordering in all
 #' trees (required if your trees don't have their leaves ordered identically).
 #' Default to \code{FALSE}.
 #'
@@ -142,7 +142,7 @@ treediff <- function(trees1, trees2, replicates, scale = FALSE,
   coph_dist <- sapply(trees, cophenetic, simplify = FALSE)
 
   # Normalize
-  if (scale) {
+  if (scale == TRUE) {
     coph_dist <- normalize_trees(coph_dist)
   }
 
@@ -174,7 +174,7 @@ treediff <- function(trees1, trees2, replicates, scale = FALSE,
   # Aggregate p-values
   out_aggr <- suppressWarnings(outp %>%
     group_by(.data$cluster) %>%
-    summarise("p.value" = min(sort(.data$p.value) / (1:.data$p)) * .data$p, 
+    summarise("p.value" = min(sort(.data$p.value) / (1:.data$p)) * .data$p,
               .groups = "keep") %>%
     unique())
 

man/treediff.Rd

@@ -27,10 +27,10 @@ different from that of \code{trees1}.}
 for each condition.}
 
 \item{scale}{Logical. If \code{TRUE}, the trees are all rescaled to have a
-minimum height equal to 0 and a maximum height equal to 1. Default to 
+minimum height equal to 0 and a maximum height equal to 1. Default to
 \code{FALSE}.}
 
-\item{order_labels}{Logical. If \code{TRUE}, align leaves ordering in all 
+\item{order_labels}{Logical. If \code{TRUE}, align leaves ordering in all
 trees (required if your trees don't have their leaves ordered identically).
 Default to \code{FALSE}.}
 

tests/testthat/test-treediff.R

@@ -86,7 +86,7 @@ test_that("Test errors", {
   # Test if the number of leaves in each cluster is the same between the two
   # sets of trees
   trees2[[5]]$order <- c(trees2[[5]]$order, 101)
-  expect_error(treediff(trees1, trees2, c(4, 6)), 
+  expect_error(treediff(trees1, trees2, c(4, 6)),
                "the number of leaves in one or more clusters is different between the two sets of trees.")
 })
 
@@ -129,3 +129,44 @@ test_that("Test for compute_pvalue", {
   expect_length(pvals$p.value, 1225)
   expect_length(pvals, 4)
 })
+
+# Test for the scale argument
+test_that("Test for the scale argument", {
+
+  # Perform the treediff test with scaling
+  res <- treediff(trees1, trees2, replicates, scale = TRUE)
+
+  # Check the output object has the expected names
+  expect_named(res, c("method", "data.name", "p.value",
+                      "statistic", "p.value.indiv"))
+
+  # Perform the treediff test without scaling
+  result1 <- treediff(trees1, trees2, replicates)
+  result2 <- treediff(trees1, trees2, replicates, scale = FALSE)
+  result3 <- treediff(trees1, trees2, replicates, scale = 5)
+
+  expect_equal(result1, result2)
+  expect_equal(result1, result3)
+})
+
+# Test for the order_labels argument
+test_that("Test for the order_labels argument", {
+
+  # Perform the treediff test with ordering the labels without labels
+  expect_error(treediff(trees1, trees2, replicates, order_labels = TRUE))
+
+  # Create a set of trees with different leaf orders
+  trees1 <- list(hclust(dist(mtcars[, 1:2]), method = "ward.D2"),
+                 hclust(dist(mtcars[, 3:4]), method = "ward.D2"))
+  trees2 <- list(hclust(dist(mtcars[, 5:6]), method = "ward.D2"),
+                 hclust(dist(mtcars[, 7:8]), method = "ward.D2"))
+
+  # Perform the treediff test with and without ordering the labels
+  res1 <- treediff(trees1, trees2, c(2,2), order_labels = TRUE)
+  res2 <- treediff(trees1, trees2, c(2,2), order_labels = FALSE)
+
+  # Test that the p-values are the same for both tests
+  expect_equal(res1, res2)
+})
+
+