tests/testthat/test_seurat.R

In PMBio/muon.r: Save Multimodal Data to h5mu Files

context("Creating .h5mu files from Seurat objects")
library(Seurat)
library(muon)
library(hdf5r)
library(fs)  # for file_temp()

fileh5mu <- paste0(file_temp(), ".h5mu")

true_val <- 0.1234569
true_val_i <- 3
true_val_j <- 7

test_that("a model can be created from a simple Seurat object", {

    x <- matrix(rnorm(1000), ncol = 100)
    y <- matrix(rnorm(2000), ncol = 100)
    obs_names <- paste("obs", 1:100, sep = "-")

    colnames(x) <- obs_names
    colnames(y) <- obs_names

    rownames(x) <- paste("x-var", 1:10, sep = "-")
    rownames(y) <- paste("y-var", 1:20, sep = "-")

    # Inject a value to be checked later
    x[true_val_i, true_val_j] <- true_val

    assay_x <- CreateAssayObject(counts = x)
    assay_y <- CreateAssayObject(counts = y)

    srt <- CreateSeuratObject(assay_x, assay = "x")
    srt[["y"]] <- assay_y

    # Add data
    srt[["x"]]@data <- x
    srt[["y"]]@data <- y
    
    # Writing
    outfile <- fileh5mu
    result <- WriteH5MU(srt, outfile)

    # Assert the data is saved
    expect_true(result)

    # Read back
    h5 <- H5File$new(outfile, mode="r")

    # Check all the assays are written
    assays <- h5[['mod']]$names
    assays_orig <- sort(names(srt))
    expect_equal(assays, assays_orig)

    h5$close_all()
})


test_that("a Seurat object can be created from an .h5mu file", {
    srt <- ReadH5MU(fileh5mu, "seurat")
    expect_equal(names(srt)[1], "x")
    expect_equal(names(srt)[2], "y")
})

test_that("values in sparse count matrices are properly recovered", {
    srt <- ReadH5MU(fileh5mu, "seurat")
    expect_equal(srt[["x"]]@counts[true_val_i, true_val_j], true_val)
    expect_equal(srt[["x"]]@data[true_val_i, true_val_j], true_val)
})