tests/testthat/test-spatialGraphs.R

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

# Unit test spatialGraphs getters and setters
library(SingleCellExperiment)
sfe2 <- readRDS(system.file("extdata/sfe_multi_sample.rds",
    package = "SpatialFeatureExperiment"
))
cgr1 <- readRDS(system.file("extdata/colgraph1.rds",
    package = "SpatialFeatureExperiment"
))
cgr2 <- readRDS(system.file("extdata/colgraph2.rds",
    package = "SpatialFeatureExperiment"
))
agr1 <- readRDS(system.file("extdata/annotgraph1.rds",
    package = "SpatialFeatureExperiment"
))
agr2 <- readRDS(system.file("extdata/annotgraph2.rds",
    package = "SpatialFeatureExperiment"
))

test_that("Set all applicable sample_ids and margins", {
    spatialGraphs(sfe2) <- list(
        sample01 = list(
            col = list(foo = cgr1),
            annot = list(bar = agr1)
        ),
        sample02 = list(
            col = list(bar = cgr2),
            annot = list(foo = agr2)
        )
    )
    df <- int_metadata(sfe2)$spatialGraphs
    expect_true(is(df, "DFrame"))
    expect_equal(names(df), c("sample01", "sample02"))
    expect_equal(rownames(df), c("row", "col", "annot"))
    expect_true(is.null(df[1, 1][[1]]))
    expect_equal(df[2, 1][[1]]$foo, cgr1)
    expect_equal(df[2, 2][[1]]$bar, cgr2)
    expect_equal(df[3, 1][[1]]$bar, agr1)
    expect_equal(df[3, 2][[1]]$foo, agr2)
})

test_that("Set all applicable sample_ids in one margin", {
    # spatialGraphs absent
    spatialGraphs(sfe2, MARGIN = 2L) <- list(
        sample01 = list(
            foo = cgr1,
            bar = cgr1
        ),
        sample02 = list(baz = cgr2)
    )
    df <- int_metadata(sfe2)$spatialGraphs
    expect_true(is(df, "DFrame"))
    expect_equal(names(df), c("sample01", "sample02"))
    expect_equal(rownames(df), c("row", "col", "annot"))
    expect_true(is.null(df[1, 1][[1]]))
    expect_equal(df[2, 1][[1]]$foo, cgr1)
    expect_equal(df[2, 1][[1]]$bar, cgr1)
    expect_equal(df[2, 2][[1]]$baz, cgr2)
    # spatialGraphs present
    spatialGraphs(sfe2, MARGIN = 3L) <- list(sample02 = list(foo = agr2))
    df <- int_metadata(sfe2)$spatialGraphs
    expect_equal(df[3, "sample02"][[1]]$foo, agr2)
})

test_that("Set all applicable margins in one sample_id", {
    spatialGraphs(sfe2, sample_id = "sample01") <- list(
        col = list(foo = cgr1),
        annot = list(
            bar = agr1,
            baz = agr1
        )
    )
    df <- int_metadata(sfe2)$spatialGraphs
    expect_true(is(df, "DFrame"))
    expect_equal(names(df), c("sample01", "sample02"))
    expect_equal(rownames(df), c("row", "col", "annot"))
    expect_true(is.null(df[1, 1][[1]]))
    expect_equal(df[2, 1][[1]]$foo, cgr1)
    expect_equal(df[3, 1][[1]]$bar, agr1)
    expect_equal(df[3, 1][[1]]$baz, agr1)
})

test_that("Set all items in one margin and one sample_id", {
    spatialGraphs(sfe2, MARGIN = 2L, sample_id = "sample02") <-
        list(foo = cgr2, bar = cgr2)
    df <- int_metadata(sfe2)$spatialGraphs
    expect_true(is(df, "DFrame"))
    expect_equal(names(df), c("sample01", "sample02"))
    expect_equal(rownames(df), c("row", "col", "annot"))
    expect_true(is.null(df[2, 1][[1]]))
    expect_equal(df[2, 2][[1]]$foo, cgr2)
    expect_equal(df[2, 2][[1]]$bar, cgr2)
})

test_that("Set graph of the same name for multiple sample_ids", {
    value <- list(sample01 = cgr1, sample02 = cgr2)
    spatialGraphs(sfe2, MARGIN = 2L, sample_id = "all", name = "foo") <- value
    expect_equal(spatialGraphNames(sfe2, 2, "sample01"), "foo")
    expect_equal(spatialGraphNames(sfe2, 2, "sample02"), "foo")
    expect_equal(spatialGraph(sfe2, "foo", 2, "sample01"), cgr1)
    expect_equal(spatialGraph(sfe2, "foo", 2, "sample02"), cgr2)
})

test_that("Set one item in one margin and one sample_id", {
    spatialGraph(sfe2, "foo", 3L, "sample01") <- agr1
    df <- int_metadata(sfe2)$spatialGraphs
    expect_true(is(df, "DFrame"))
    expect_equal(names(df), c("sample01", "sample02"))
    expect_equal(rownames(df), c("row", "col", "annot"))
    expect_true(is.null(df[2, 1][[1]]))
    expect_equal(df[3, 1][[1]]$foo, agr1)
    # Use integer index
    spatialGraph(sfe2, 1L, 3L, "sample01") <- agr2
    df <- int_metadata(sfe2)$spatialGraphs
    expect_equal(df[3, 1][[1]][[1]], agr2, ignore_attr = "call")
    # Error when wrong length
    expect_error(
        spatialGraph(sfe2, "foo", 2L, "sample01") <- cgr2,
        "number of samples"
    )
    # Error when not listw
    expect_error(
        spatialGraph(sfe2, "foo", 3L, "sample01") <- "foobar",
        "listw"
    )
})

# If it passes the above tests, then the setters should work. Then I'll use the
# setter rather than to use int_metadata to unit test the getters.
spatialGraphs(sfe2) <- list(
    sample01 = list(
        col = list(foo = cgr1),
        annot = list(bar = agr1)
    ),
    sample02 = list(
        col = list(bar = cgr2),
        annot = list(foo = agr2)
    )
)
mar_names <- c("row", "col", "annot")
test_that("Get all applicable sample_ids and margins", {
    out_all <- spatialGraphs(sfe2)
    expect_equal(names(out_all), c("sample01", "sample02"))
    expect_equal(names(out_all[[1]]), mar_names)
    expect_equal(names(out_all[[2]]), mar_names)
    expect_true(is.null(out_all$sample01$row))
    expect_equal(names(out_all$sample01$col), "foo")
    expect_equal(names(out_all$sample02$annot), "foo")
    expect_equal(out_all$sample01$col$foo, cgr1)
    expect_equal(out_all$sample02$annot$foo, agr2)
})

test_that("Get all applicable sample_ids in one margin", {
    out_mar1 <- spatialGraphs(sfe2, 1)
    expect_equal(names(out_mar1), c("sample01", "sample02"))
    expect_true(is.null(out_mar1$sample01))
    expect_true(is.null(out_mar1$sample02))

    out_mar2 <- spatialGraphs(sfe2, 2)
    expect_equal(names(out_mar2), c("sample01", "sample02"))
    expect_equal(names(out_mar2$sample01), "foo")
    expect_equal(out_mar2$sample02$bar, cgr2)

    out_mar3 <- spatialGraphs(sfe2, 3)
    expect_equal(names(out_mar3), c("sample01", "sample02"))
    expect_equal(names(out_mar3$sample01), "bar")
    expect_equal(out_mar3$sample02$foo, agr2)
})

test_that("Set all applicable margins in one sample_id", {
    out_sample02 <- spatialGraphs(sfe2, sample_id = "sample02")
    expect_equal(names(out_sample02), mar_names)
    expect_true(is.null(out_sample02$row))
    expect_equal(out_sample02$col$bar, cgr2)
    expect_equal(out_sample02$annot$foo, agr2)
})

test_that("Get all items in one margin and one sample_id", {
    out <- spatialGraphs(sfe2, 3, "sample01")
    expect_true(is.list(out))
    expect_equal(names(out), "bar")
    expect_equal(out$bar, agr1)
    # Make sure that it still works for one sample
    # I got into some troubles with this
    sfe <- sfe2[, colData(sfe2)$sample_id == "sample01"]
    out <- spatialGraphs(sfe2, 3, "sample01")
    expect_true(is.list(out))
    expect_equal(names(out), "bar")
    expect_equal(out$bar, agr1)
})

test_that("Get graphs of the same name from multiple samples", {
    colGraph(sfe2, "foo", sample_id = "sample02") <- cgr2
    out <- spatialGraphs(sfe2, 2, sample_id = "all", name = "foo")
    expect_true(is.list(out))
    expect_equal(length(out), 2L)
    expect_equal(names(out), c("sample01", "sample02"))
    expect_s3_class(out[[1]], "listw")
    expect_s3_class(out[[2]], "listw")
    # Still works with one sample
    sfe <- sfe2[, colData(sfe2)$sample_id == "sample01"]
    out <- spatialGraphs(sfe, 2, sample_id = "sample01", name = "foo")
    expect_true(is.list(out))
    expect_equal(length(out), 1L)
    expect_equal(names(out), "sample01")
    expect_s3_class(out[[1]], "listw")
})

test_that("Get one item in one margin and one sample_id", {
    out <- spatialGraph(sfe2, "foo", 2, "sample01")
    expect_equal(out, cgr1)
    # When the requested item doesn't exist
    expect_error(spatialGraph(sfe2, "bar", 1, "sample01"), "is absent")
})

test_that("spatialGraphNames getter", {
    expect_equal(spatialGraphNames(sfe2, 2, "sample01"), "foo")
})

test_that("spatialGraphNames setter", {
    spatialGraphNames(sfe2, 2, "sample01") <- "meow"
    expect_equal(
        names(int_metadata(sfe2)$spatialGraphs["col", "sample01"][[1]]),
        "meow"
    )
})

test_that("Set all graphs to NULL", {
    spatialGraphs(sfe2) <- NULL
    empty <- SpatialFeatureExperiment:::.initialize_spatialGraphs(sfe2)
    expect_equal(int_metadata(sfe2)$spatialGraphs, empty)
})

test_that("Set all graphs in one margin to NULL", {
    spatialGraphs(sfe2, 3) <- NULL
    expect_true(is.null(unlist(as.list(int_metadata(sfe2)$spatialGraphs[3, ]))))
})

test_that("Set all graphs in one sample_id to NULL", {
    spatialGraphs(sfe2, sample_id = "sample01") <- NULL
    expect_true(is.null(unlist(as.list(int_metadata(sfe2)$spatialGraphs[, 1]))))
})

test_that("Set all graphs in one margin of one sample_id to NULL", {
    spatialGraphs(sfe2, 3, "sample01") <- NULL
    expect_true(is.null(unlist(int_metadata(sfe2)$spatialGraphs[3, 1])))
})

test_that("Remove one graph from one margin and one sample_id", {
    spatialGraph(sfe2, "foo", 3, "sample02") <- NULL
    expect_true(is.null(int_metadata(sfe2)$spatialGraphs[3, 2][["foo"]]))
})