tests/testthat/test-validity.R

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

# Unit test validity functions
library(sf)
library(SingleCellExperiment)

sfe <- readRDS(system.file("extdata/sfe_toy.rds",
    package = "SpatialFeatureExperiment"
))
cg_toy <- readRDS(system.file("extdata/cg_toy.rds",
    package = "SpatialFeatureExperiment"
))
cg_toy2 <- readRDS(system.file("extdata/cg_toy2.rds",
    package = "SpatialFeatureExperiment"
))
ag <- readRDS(system.file("extdata/ag.rds",
    package = "SpatialFeatureExperiment"
))
cgr1 <- readRDS(system.file("extdata/colgraph1.rds",
    package = "SpatialFeatureExperiment"
))

test_that("Everything in *Geometries must be sf objects", {
    int_colData(sfe)$colGeometries <- make_zero_col_DFrame(nrow = ncol(sfe))
    int_colData(sfe)$colGeometries$coords <- cg_toy
    expect_true(validObject(sfe))
    int_colData(sfe)$colGeometries$coords <- st_drop_geometry(cg_toy)
    expect_error(validObject(sfe), "rather\\s+than\\s+sf")
})

test_that("All sample_ids in annotGeometries must be present in colData", {
    int_metadata(sfe)$annotGeometries$foo <- ag
    expect_true(validObject(sfe))
    ag$sample_id <- "foo"
    int_metadata(sfe)$annotGeometries$foo <- ag
    expect_error(validObject(sfe), "absent from colData")
    ag$sample_id <- NULL
    int_metadata(sfe)$annotGeometries$foo <- ag
    expect_error(validObject(sfe), "does not have column sample_id")
})

test_that("All graphs must be listw objects", {
    expect_error(spatialGraphs(sfe, MARGIN = 3, sample_id = "sample01") <-
        list(foo = "bar"), "must have class listw")
})

test_that("All row and col graphs must have the right number of nodes", {
    expect_error(spatialGraphs(sfe, MARGIN = 2, sample_id = "sample01") <-
        list(foo = cgr1), "do not have the right length")
})

test_that("The spatialGraphs field must have the right structure", {
    int_metadata(sfe)$spatialGraphs <- list(foo = "bar")
    expect_error(validObject(sfe), "must be a DataFrame")
    df <- SpatialFeatureExperiment:::.initialize_spatialGraphs(sfe)
    names(df) <- "foo"
    int_metadata(sfe)$spatialGraphs <- df
    expect_error(validObject(sfe), "but not colData")
    names(df) <- "sample01"
    rownames(df) <- c("foo", "bar", "baz")
    int_metadata(sfe)$spatialGraphs <- df
    expect_error(validObject(sfe), "Row names")
})