Adapt tests

Author: csoneson

tests/testthat/test-utilities.R

@@ -63,19 +63,46 @@ test_that("get_count_datasets works", {
     expect_equal(cds$mat2, seq(10, 18))
     expect_equal(cds$mat3, seq(19, 27))
 
-    # SE does not have dimnames, two assays have the same, third assay does not have -> error
+    # SE does not have dimnames, assays 1 and 3 have the same, assay 2 does not have
+    # SE dimnames will be set to those of assay 1, then assay 2 dimnames to those of the SE
     se1 <- se
     rownames(se1) <- colnames(se1) <- NULL
     rownames(assay(se1, "mat2", withDimnames = FALSE)) <- 
         colnames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
-    expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names")
+    expect_warning(expect_warning(expect_warning(expect_warning(cds <- get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names"))))
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 9L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
+    expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
+    expect_equal(cds$mat1, seq(1, 9))
+    expect_equal(cds$mat2, seq(10, 18))
+    expect_equal(cds$mat3, seq(19, 27))
+    
+    # SE does not have dimnames, assays 2 and 3 have the same, assay 1 does not have
+    # SE dimnames will be set to those of assay 2, then assay 1 dimnames to those of the SE
+    se1 <- se
+    rownames(se1) <- colnames(se1) <- NULL
+    rownames(assay(se1, "mat1", withDimnames = FALSE)) <- 
+        colnames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
+    expect_warning(expect_warning(expect_warning(expect_warning(cds <- get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names"))))
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 9L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
+    expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
+    expect_equal(cds$mat1, seq(1, 9))
+    expect_equal(cds$mat2, seq(10, 18))
+    expect_equal(cds$mat3, seq(19, 27))
 
     # SE does not have dimnames, assays have the same but in different order
     se1 <- se
     rownames(se1) <- colnames(se1) <- NULL
     colnames(assay(se1, "mat2", withDimnames = FALSE)) <- c("S2", "S3", "S1")
     rownames(assay(se1, "mat3", withDimnames = FALSE)) <- c("G2", "G3", "G1")
-    expect_warning(expect_warning(cds <- get_count_datasets(se1), "have column names, but the SummarizedExperiment does not"), "have row names, but the SummarizedExperiment does not")
+    expect_warning(expect_warning(cds <- get_count_datasets(se1)))
     expect_s3_class(cds, "tbl_df")
     expect_equal(nrow(cds), 9L)
     expect_equal(ncol(cds), 5L)
@@ -86,16 +113,38 @@ test_that("get_count_datasets works", {
     expect_equal(cds$mat2, c(16, 17, 18, 10, 11, 12, 13, 14, 15))
     expect_equal(cds$mat3, c(21, 19, 20, 24, 22, 23, 27, 25, 26))
 
-    # SE does not have dimnames, assays have nonoverlapping dimnames -> error
+    # SE does not have dimnames, assays have nonoverlapping dimnames
+    ## ...rownames
     se1 <- se
     rownames(se1) <- colnames(se1) <- NULL
     rownames(assay(se1, "mat2", withDimnames = FALSE)) <- paste0("A", seq_len(3))
-    expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have row names")
+    expect_warning(expect_warning(expect_warning(cds <- get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have row names")))
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 18L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, c(rep(paste0("G", seq_len(3)), 3), 
+                                 rep(paste0("A", seq_len(3)), 3)))
+    expect_equal(cds$.sample, rep(rep(paste0("S", seq_len(3)), each = 3), 2))
+    expect_equal(cds$mat1, c(seq(1, 9), rep(NA, 9)))
+    expect_equal(cds$mat2, c(rep(NA, 9), seq(10, 18)))
+    expect_equal(cds$mat3, c(seq(19, 27), rep(NA, 9)))
 
+    ## ...colnames
     se1 <- se
     rownames(se1) <- colnames(se1) <- NULL
     colnames(assay(se1, "mat2", withDimnames = FALSE)) <- paste0("A", seq_len(3))
-    expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names")
+    expect_warning(expect_warning(expect_warning(cds <- get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names")))
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 18L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, rep(rep(paste0("G", seq_len(3)), 3), 2))
+    expect_equal(cds$.sample, c(rep(paste0("S", seq_len(3)), each = 3),
+                                rep(paste0("A", seq_len(3)), each = 3)))
+    expect_equal(cds$mat1, c(seq(1, 9), rep(NA, 9)))
+    expect_equal(cds$mat2, c(rep(NA, 9), seq(10, 18)))
+    expect_equal(cds$mat3, c(seq(19, 27), rep(NA, 9)))
 
     # Neither SE nor assays have column names
     se1 <- se
@@ -155,11 +204,29 @@ test_that("get_count_datasets works", {
     # SE has dimnames, assays have the same dimnames but not overlapping with those of the SE
     se1 <- se
     rownames(se1) <- colnames(se1) <- paste0("A", seq_len(3))
-    expect_error(get_count_datasets(se1), "don't agree with the column names of the SummarizedExperiment")
+    expect_warning(expect_warning(cds <- get_count_datasets(se1), "don't agree with the column names of the SummarizedExperiment"))
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 9L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
+    expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
+    expect_equal(cds$mat1, seq(1, 9))
+    expect_equal(cds$mat2, seq(10, 18))
+    expect_equal(cds$mat3, seq(19, 27))
 
     se1 <- se
     rownames(se1) <- paste0("A", seq_len(3))
-    expect_error(get_count_datasets(se1), "don't agree with the row names of the SummarizedExperiment")
+    expect_warning(cds <- get_count_datasets(se1), "don't agree with the row names of the SummarizedExperiment")
+    expect_s3_class(cds, "tbl_df")
+    expect_equal(nrow(cds), 9L)
+    expect_equal(ncol(cds), 5L)
+    expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
+    expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
+    expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
+    expect_equal(cds$mat1, seq(1, 9))
+    expect_equal(cds$mat2, seq(10, 18))
+    expect_equal(cds$mat3, seq(19, 27))
 
     # SE has dimnames, none of the assays have
     se1 <- se