tests/testthat/test-df2sf.R

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

library(sf)
pts_df <- readRDS(system.file("extdata/pts_df.rds",
    package = "SpatialFeatureExperiment"
))
pts_sf <- readRDS(system.file("extdata/pts_sf.rds",
                              package = "SpatialFeatureExperiment"
))
test_that("df2sf works properly for points", {
    sf_use <- df2sf(pts_df, geometryType = "POINT")
    expect_equal(sf_use, pts_sf, ignore_attr = TRUE)
})

test_that("Points but with spotDiameter", {
    sf_use <- df2sf(pts_df, geometryType = "POINT", spotDiameter = 0.1)
    expect_warning(df2sf(pts_df, geometryType = "POINT", spotDiameter = 0.1,
                         BPPARAM = BiocParallel::SerialParam()), "deprecated")
    pts_sf_dia <- readRDS(system.file("extdata/pts_sf_dia.rds",
        package = "SpatialFeatureExperiment"
    ))
    expect_equal(sf_use, pts_sf_dia, ignore_attr = TRUE)
})

test_that("Multipoints", {
    multipts_df <- readRDS(system.file("extdata/multipts_df.rds",
        package = "SpatialFeatureExperiment"
    ))
    multipts_df$ID <- NULL # shouldn't be required
    sf_use <- df2sf(multipts_df, geometryType = "MULTIPOINT")
    multipts_sf <- readRDS(system.file("extdata/multipts_sf.rds",
        package = "SpatialFeatureExperiment"
    ))
    names(sf_use)[1] <- "ID"
    sf_use <- sf_use[, names(multipts_sf)]
    expect_equal(sf_use, multipts_sf, ignore_attr = TRUE)
})

test_that("Linestring", {
    ls_df <- readRDS(system.file("extdata/ls_df.rds",
        package = "SpatialFeatureExperiment"
    ))
    sf_use <- df2sf(ls_df, geometryType = "LINESTRING")
    ls_sf <- readRDS(system.file("extdata/ls_sf.rds",
        package = "SpatialFeatureExperiment"
    ))
    expect_equal(sf_use, ls_sf, ignore_attr = TRUE)
})

test_that("Not enough vertices for the specified geometry", {
    ls_df_singleton <- readRDS(system.file("extdata/ls_df_singleton.rds",
        package = "SpatialFeatureExperiment"
    ))
    expect_warning(
        sf_use <- df2sf(ls_df_singleton, geometryType = "LINESTRING"),
        "Removed"
    )
    ls_sf_singleton <- readRDS(system.file("extdata/ls_sf_singleton.rds",
        package = "SpatialFeatureExperiment"
    ))
    expect_equal(sf_use, ls_sf_singleton, ignore_attr = TRUE)
})

test_that("Multilinestring", {
    multils_df <- readRDS(system.file("extdata/multils_df.rds",
        package = "SpatialFeatureExperiment"
    ))
    multils_sf <- readRDS(system.file("extdata/multils_sf.rds",
        package = "SpatialFeatureExperiment"
    ))
    sf_use <- df2sf(multils_df, geometryType = "MULTILINESTRING")
    expect_equal(multils_sf, sf_use, ignore_attr = TRUE)
})

test_that("Polygons", {
    pol_df <- readRDS(system.file("extdata/pol_df.rds",
        package = "SpatialFeatureExperiment"
    ))
    sf_use <- df2sf(pol_df,
        geometryType = "POLYGON",
        spatialCoordsNames = c("V1", "V2")
    )
    pol_sf <- readRDS(system.file("extdata/pol_sf.rds",
        package = "SpatialFeatureExperiment"
    ))
    sf_use <- sf_use[, names(pol_sf)]
    expect_equal(pol_sf, sf_use, ignore_attr = TRUE)
})

test_that("De facto points get POINT geometry", {
    sf_use <- df2sf(pts_df, geometryType = "POLYGON")
    expect_true(all(st_is(sf_use, "POINT")))
    expect_equal(sf_use, pts_sf, ignore_attr = TRUE)
})

test_that("Multipolygons", {
    mpol_df <- readRDS(system.file("extdata/mpol_df.rds",
        package = "SpatialFeatureExperiment"
    ))
    mpol_sf <- readRDS(system.file("extdata/mpol_sf.rds",
        package = "SpatialFeatureExperiment"
    ))
    sf_use <- df2sf(mpol_df,
        geometryType = "MULTIPOLYGON",
        spatialCoordsNames = c("V1", "V2")
    )
    names(sf_use)[1] <- "ID"
    sf_use <- sf_use[, names(mpol_sf)]
    expect_equal(sf_use, mpol_sf, ignore_attr = TRUE)
})

test_that("When there're other attributes", {
    # One unique set per geometry
    pol_df <- readRDS(system.file("extdata/pol_df.rds",
                                  package = "SpatialFeatureExperiment"
    ))
    pol_df$foo <- rep("D", nrow(pol_df))
    sf_use <- df2sf(pol_df,
                    geometryType = "POLYGON",
                    spatialCoordsNames = c("V1", "V2")
    )
    expect_true(setequal(names(sf_use), c("ID", "foo", "geometry")))
    expect_equal(sf_use$foo, "D")
})

test_that("Drop columns with multiple combinations per geometry", {
    pol_df <- readRDS(system.file("extdata/pol_df.rds",
                                  package = "SpatialFeatureExperiment"
    ))
    pol_df$foo <- c(rep("C", 4), rep("D", 4))
    sf_use <- df2sf(pol_df,
                    geometryType = "POLYGON",
                    spatialCoordsNames = c("V1", "V2")
    )
    expect_true(setequal(names(sf_use), c("ID", "geometry")))
})