DRAFT: Test/simplify transformation tests

tests/testthat/test-5transformCounts.R

@@ -134,50 +134,18 @@ test_that("transformAssay", {
         expect_equal(typeof(actual),"double")
         expect_true(all(actual == 1 | actual == 0))
 
-        ######################## HELLINGER #####################################
-        # Calculates Hellinger transformation. Should be equal.
-        # Calculates relative abundance table
-        relative <- assays(mia::transformAssay(tse, method = "relabundance", name = "relative"))$relative
-
-        expect_equal(as.matrix(assays(mia::transformAssay(tse, method = "hellinger", name = "test_123"))$test_123),
-                     apply(as.matrix(relative), 2, FUN=function(x){
-                         sqrt(x)
-                     }), check.attributes = FALSE)
-
         ############################### CLR ####################################
-        # Calculates clr-transformation. Should be equal.
-
         # Random pseudocount
         pseudonumber <- runif(1, 1, 100)
 
         tse <- transformAssay(tse, method = "relabundance")
-        # Calculates relative abundance table
-        relative <- assay(tse, "relabundance")
-        relative <- relative + pseudonumber
-        # Tests clr
-        # Calc CLRs
-        mat <- assays(mia::transformAssay(tse, assay.type = "relabundance",
-                                           method = "clr", pseudocount = pseudonumber))$clr
-        mat_comp <- apply(as.matrix(relative), 2, FUN=function(x){
-            log(x) - mean(log(x))
-        })
-        # Remove attributes since vegan adds additional ones
-        attributes(mat) <- NULL
-        attributes(mat_comp) <- NULL
-        # Compare
-        expect_equal(mat, mat_comp)
-
-        # Expect that error occurs
-        expect_error(mia::transformAssay(tse, method = "clr"))
 
         # Expect that error does not occur
         tse <- mia::transformAssay(tse, method = "rclr")
 
         # Tests transformAssay, tries to calculate clr. Should be an error, because of zeros.
         expect_error(mia::transformAssay(tse, method = "clr"))
 
-        # Tests that clr robust gives values that are approximately same if only
-        # one value per sample are changed to zero
         tse <- transformAssay(tse, method = "relabundance")
         # Adds pseudocount
         assay(tse, "test") <- assay(tse, "relabundance") + 1
@@ -188,6 +156,15 @@ test_that("transformAssay", {
         assay(tse, "test2")[1, ] <- 0
         # One missing value
         assay(tse, "na_values")[4, 5] <- NA
+
+        # Tests that clr robust gives values that are approximately same if only
+        # one value per sample is changed to zero
+        expect_equal(assays(mia::transformAssay(tse, assay.type = "test",
+                                                method = "rclr")),
+                     assays(mia::transformAssay(tse, assay.type = "test2",
+                                                method = "rclr")),
+                     check.attributes = FALSE)
+
 
         tse <- transformAssay(tse, method = "relabundance")
         # Expect error when counts and zeroes
@@ -272,18 +249,6 @@ test_that("transformAssay", {
         # Expect that assay contains count and rank table
         expect_true(all(c("counts", "rank") %in% assayNames(tse_rank)))
 
-        for(i in c(1:10)){
-            # Gets columns from 'rank' table
-            ranks <- assay(tse_rank, "rank")[,i]
-            # Gets columns from 'counts' table, and calculates ranks
-            counts_compare <- assay(tse_rank, "counts")[,i]
-            counts_compare[counts_compare == 0] <- NA
-            ranks_compare <- rank(counts_compare, na.last = "keep")
-            ranks_compare[is.na(ranks_compare)] <- 0
-            # Expect that they are equal
-            expect_equal(ranks, ranks_compare, check.attributes = FALSE)
-        }
-
         # Calculates rank with pseudocount
         tse_rank_pseudo <- transformAssay(tse, method = "rank", pseudocount = runif(1, 0, 1000))
         # Pseudocount should not change the rank
@@ -304,6 +269,7 @@ test_that("transformAssay", {
         expect_equal(max(abs(z_assay - xx), na.rm=TRUE), 0,
                      tolerance = 1e-14, check.attributes = FALSE)
 
+        ####################### Test equality to vegan #########################
         # Test that transformations are equal to ones directly from vegan
         # clr
         tse <- transformAssay(tse, method = "relabundance")
@@ -313,9 +279,9 @@ test_that("transformAssay", {
         compare <- vegan::decostand(assay(tse, "relabundance"), method = "clr",
                                     pseudocount = 4, MARGIN = 2)
         expect_equal(actual, compare)
+
         # rclr
         tse <- transformAssay(tse, assay.type = "relabundance", method = "rclr")
-
         actual <- assay(tse, "rclr")
         # mia has additional pseudocount parameter for all methods
         attr(actual, "parameters")$pseudocount <- NULL
@@ -351,6 +317,16 @@ test_that("transformAssay", {
                                     MARGIN = 2)
         compare <- t(compare)
         expect_equal(na.omit(actual), na.omit(compare))
+
+        # rank
+        tse <- transformAssay(tse, assay.type = "counts", method = "rank")
+        actual <- assay(tse, "rank")
+        attr(actual, "parameters")$pseudocount <- NULL
+        compare <- vegan::decostand(assay(tse, "counts"), method = "rank",
+                                    MARGIN = 2)
+        expect_equal(actual, compare)
+
+
 
         # Check that transformation is applied to altExps
         expect_error(transformAssay(tse, altexp = "Phylum"))
@@ -372,7 +348,7 @@ test_that("transformAssay", {
         test <- altExp(test, "Genus")
         expect_equal(assay(test, "relabundance"), assay(ref, "relabundance"))
 
-        # Check that philt transformation works
+        # Check that philr transformation works
         skip_if_not_installed("philr")
         data("GlobalPatterns")
         tse <- GlobalPatterns