tests/testthat/test-read_sparse_matrix.R

In rafalab/smallcount: Methods for Small Counts Stored in a Sparse Matrix

MATRIX_FILENAME <- "small_dense_square"

# Verifies that a SparseMatrix object read from a test file has shape 3x3 and
# contains the values 1-9 row-wise.
validate_test_matrix <- function(sparse_matrix) {
    expected_dim <- c(3, 3)
    expected_matrix <- t(matrix(c(1:9), nrow = 3, ncol = 3))
    expected_dimnames <- list(c("r1", "r2", "r3"), c("c1", "c2", "c3"))

    dim <- sparse_matrix@dim
    expect_equal(dim, expected_dim)
    expect_equal(matrix(sparse_matrix, nrow = dim[1], ncol = dim[2]), expected_matrix)
    expect_equal(sparse_matrix@dimnames, expected_dimnames)
}

test_that("Reads .h5 file (Cell Ranger v3)", {
    matrix_file <- test_path("testdata", paste0(MATRIX_FILENAME, "_v3.h5"))

    svt_matrix <- readSparseMatrix(matrix_file, col.names = TRUE)
    validate_test_matrix(svt_matrix)
})

test_that("Reads .h5 file (Cell Ranger v2)", {
    matrix_file <- test_path("testdata", paste0(MATRIX_FILENAME, "_v2.h5"))

    svt_matrix <- readSparseMatrix(matrix_file,
        col.names = TRUE,
        row.names = "symbol", genome = "genome"
    )
    validate_test_matrix(svt_matrix)
})

test_that("Reads bzipped .mtx directory (Cell Ranger v3)", {
    matrix_file <- test_path("testdata", paste0(MATRIX_FILENAME, "_v3.tbz2"))

    svt_matrix <- readSparseMatrix(matrix_file, col.names = TRUE, row.names = "id")
    validate_test_matrix(svt_matrix)
})

test_that("Reads .mtx directory with prefix (Cell Ranger v2)", {
    matrix_file <- test_path("testdata", paste0(MATRIX_FILENAME, "_v2/prefix_"))

    svt_matrix <- readSparseMatrix(matrix_file,
        col.names = TRUE,
        row.names = "symbol"
    )
    validate_test_matrix(svt_matrix)
})

test_that("Reads gzipped .csv file", {
    matrix_file <- test_path("testdata", paste0(MATRIX_FILENAME, ".tar.gz"))

    svt_matrix <- readSparseMatrix(matrix_file)
    validate_test_matrix(svt_matrix)
})