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Add unit tests for utilities
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‎tests/testthat/test-utilities.R‎

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test_that("get_count_datasets works", {
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# Use testthat edition 3
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local_edition(3)
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# Generate test SE
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se <- SummarizedExperiment::SummarizedExperiment(
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assays = list(
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mat1 = matrix(seq_len(9), nrow = 3),
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mat2 = matrix(seq(10, 18), nrow = 3),
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mat3 = matrix(seq(19, 27), nrow = 3)
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)
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)
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rownames(se) <- paste0("G", seq_len(3))
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colnames(se) <- paste0("S", seq_len(3))
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SummarizedExperiment::assays(se) <- lapply(
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SummarizedExperiment::assays(se),
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function(x) {
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rownames(x) <- rownames(se)
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colnames(x) <- colnames(se)
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x
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}
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)
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# Check that dimnames are as expected
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expect_equal(rownames(se), rownames(assay(se, "mat1", withDimnames = FALSE)))
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expect_equal(rownames(se), rownames(assay(se, "mat2", withDimnames = FALSE)))
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expect_equal(rownames(se), rownames(assay(se, "mat3", withDimnames = FALSE)))
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expect_equal(colnames(se), colnames(assay(se, "mat1", withDimnames = FALSE)))
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expect_equal(colnames(se), colnames(assay(se, "mat2", withDimnames = FALSE)))
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expect_equal(colnames(se), colnames(assay(se, "mat3", withDimnames = FALSE)))
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# Check that matrix values are as expected
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expect_equal(assay(se, "mat1")[, 1], c(1, 2, 3), ignore_attr = TRUE)
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expect_equal(assay(se, "mat2")[, 2], c(13, 14, 15), ignore_attr = TRUE)
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expect_equal(assay(se, "mat3")[, 3], c(25, 26, 27), ignore_attr = TRUE)
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# SE and all assays have the same dimnames
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cds <- get_count_datasets(se)
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
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expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# SE does not have dimnames, all assays have the same
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se1 <- se
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rownames(se1) <- colnames(se1) <- NULL
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expect_equal(colnames(assay(se1, "mat1", withDimnames = FALSE)), paste0("S", seq_len(3)))
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expect_equal(rownames(assay(se1, "mat1", withDimnames = FALSE)), paste0("G", seq_len(3)))
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expect_null(colnames(se1))
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expect_null(rownames(se1))
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expect_warning(expect_warning(cds <- get_count_datasets(se1), "have column names, but the SummarizedExperiment does not"), "have row names, but the SummarizedExperiment does not")
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
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expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# SE does not have dimnames, two assays have the same, third assay does not have -> error
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se1 <- se
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rownames(se1) <- colnames(se1) <- NULL
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rownames(assay(se1, "mat2", withDimnames = FALSE)) <-
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names")
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# SE does not have dimnames, assays have the same but in different order
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se1 <- se
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rownames(se1) <- colnames(se1) <- NULL
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- c("S2", "S3", "S1")
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rownames(assay(se1, "mat3", withDimnames = FALSE)) <- c("G2", "G3", "G1")
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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")
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
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expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, c(16, 17, 18, 10, 11, 12, 13, 14, 15))
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expect_equal(cds$mat3, c(21, 19, 20, 24, 22, 23, 27, 25, 26))
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# SE does not have dimnames, assays have nonoverlapping dimnames -> error
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se1 <- se
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rownames(se1) <- colnames(se1) <- NULL
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rownames(assay(se1, "mat2", withDimnames = FALSE)) <- paste0("A", seq_len(3))
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expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have row names")
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se1 <- se
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rownames(se1) <- colnames(se1) <- NULL
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- paste0("A", seq_len(3))
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expect_error(get_count_datasets(se1), "at least one of the assays in your SummarizedExperiment have column names")
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# Neither SE nor assays have column names
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se1 <- se
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colnames(se1) <- NULL
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colnames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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cds <- get_count_datasets(se1)
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
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expect_equal(cds$.sample, rep(as.character(seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# Neither SE nor assays have row names
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se1 <- se
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rownames(se1) <- NULL
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rownames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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cds <- get_count_datasets(se1)
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(as.character(seq_len(3)), 3))
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expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# Neither SE nor assays have any dimnames
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se1 <- se
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rownames(se1) <- NULL
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colnames(se1) <- NULL
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rownames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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cds <- get_count_datasets(se1)
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(as.character(seq_len(3)), 3))
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expect_equal(cds$.sample, rep(as.character(seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# SE has dimnames, assays have the same dimnames but not overlapping with those of the SE
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se1 <- se
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rownames(se1) <- colnames(se1) <- paste0("A", seq_len(3))
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expect_error(get_count_datasets(se1), "don't agree with the column names of the SummarizedExperiment")
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se1 <- se
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rownames(se1) <- paste0("A", seq_len(3))
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expect_error(get_count_datasets(se1), "don't agree with the row names of the SummarizedExperiment")
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# SE has dimnames, none of the assays have
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se1 <- se
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rownames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat1", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat2", withDimnames = FALSE)) <- NULL
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rownames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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colnames(assay(se1, "mat3", withDimnames = FALSE)) <- NULL
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cds <- get_count_datasets(se1)
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expect_s3_class(cds, "tbl_df")
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expect_equal(nrow(cds), 9L)
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expect_equal(ncol(cds), 5L)
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expect_named(cds, c(".feature", ".sample", "mat1", "mat2", "mat3"))
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expect_equal(cds$.feature, rep(paste0("G", seq_len(3)), 3))
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expect_equal(cds$.sample, rep(paste0("S", seq_len(3)), each = 3))
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expect_equal(cds$mat1, seq(1, 9))
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expect_equal(cds$mat2, seq(10, 18))
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expect_equal(cds$mat3, seq(19, 27))
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# Unnamed assay(s)
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# se1 <- SummarizedExperiment::SummarizedExperiment(
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# assays = list(
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# matrix(seq_len(9), nrow = 3),
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# mat2 = matrix(seq(10, 18), nrow = 3),
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# matrix(seq(19, 27), nrow = 3)
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# )
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# )
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# expect_error(cds <- get_count_datasets(se1), "assays must be named")
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#
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# se1 <- SummarizedExperiment::SummarizedExperiment(
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# assays = list(
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# matrix(seq_len(9), nrow = 3),
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# matrix(seq(10, 18), nrow = 3),
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# matrix(seq(19, 27), nrow = 3)
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# )
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# )
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# expect_error(cds <- get_count_datasets(se1), "assays must be named")
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})

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