test_that("spatial neighbors", {

  # get data

  data("xenium_data")

  # spatial neighbors, delaunay

  xenium_data <- getSpatialNeighbors(xenium_data, method = "delaunay", verbose = FALSE)

  graphs <- vrGraph(xenium_data, graph.type = "delaunay")

  expect_true(inherits(graphs,"igraph"))

  expect_true(length(igraph::E(graphs)) > 0)

  vrSpatialPlot(xenium_data, graph.name = "delaunay", group.by = "clusters")

  # spatial neighbors, spatialkNN

  xenium_data <- getSpatialNeighbors(xenium_data, method = "spatialkNN", k = 5, verbose = FALSE)

  graphs <- vrGraph(xenium_data, graph.type = "spatialkNN")

  expect_true(inherits(graphs,"igraph"))

  expect_true(length(igraph::E(graphs)) > 0)

  vrSpatialPlot(xenium_data, graph.name = "spatialkNN", group.by = "clusters")

  # spatial neighbors, radius

  xenium_data <- getSpatialNeighbors(xenium_data, method = "radius", radius = 10, verbose = FALSE)

  graphs <- vrGraph(xenium_data, graph.type = "radius")

  expect_true(inherits(graphs,"igraph"))

  expect_true(length(igraph::E(graphs)) > 0)

  vrSpatialPlot(xenium_data, graph.name = "radius", group.by = "clusters")

  # return

  expect_equal(1,1L)

})

test_that("spatial neighbors for subsets", {

  # get data

  data("xenium_data")

  # merge two of same types

  xenium_data2 <- xenium_data

  xenium_data2$Sample <- "XeniumR2"

  merged_data <- merge(xenium_data, xenium_data2, verbose = FALSE)

  # spatial neighbors, delaunay

  merged_data <- getSpatialNeighbors(merged_data, assay = "Assay1", method = "delaunay", verbose = FALSE)

  graphs <- vrGraph(merged_data, graph.type = "delaunay")

  expect_true(inherits(graphs,"igraph"))

  expect_true(length(igraph::E(graphs)) > 0)

  vrSpatialPlot(merged_data, graph.name = "delaunay", group.by = "clusters")

  # return

  expect_equal(1,1L)

})

test_that("spatial tests", {

  # get data

  data("xenium_data")

  # spatial neighbors, radius based

  xenium_data <- getSpatialNeighbors(xenium_data, method = "radius", radius = 10, verbose = FALSE)

  # getis ord test

  xenium_data <- getHotSpotAnalysis(xenium_data, graph.type = "radius", features = c("GNLY"), verbose = FALSE)

  expect_true(all(c("GNLY_hotspot_stat", "GNLY_hotspot_pvalue", "GNLY_hotspot_flag") %in% colnames(Metadata(xenium_data))))

  xenium_data <- getHotSpotAnalysis(xenium_data, graph.type = "radius", features = c("GNLY", "Count"), verbose = FALSE)

  expect_error(getHotSpotAnalysis(xenium_data, graph.type = "radius", features = c("GNLY", "Count1"), verbose = FALSE))

  expect_error(getHotSpotAnalysis(xenium_data, graph.type = "radius", features = c("GNLY2", "Count1"), verbose = FALSE))

  # multiple assays

  data("xenium_data")

  xenium_data2 <- xenium_data

  xenium_data2$Sample <- "Sample2"

  xenium_data <- merge(xenium_data, xenium_data2, verbose = FALSE)

  xenium_data <- getSpatialNeighbors(xenium_data, method = "radius", radius = 10, verbose = FALSE)

  xenium_data <- getHotSpotAnalysis(xenium_data, graph.type = "radius", features = c("GNLY", "Count"), verbose = FALSE)

  expect_true(all(c("GNLY_hotspot_stat", "GNLY_hotspot_pvalue", "GNLY_hotspot_flag") %in% colnames(Metadata(xenium_data))))

  expect_true(all(c("Count_hotspot_stat", "Count_hotspot_pvalue", "Count_hotspot_flag") %in% colnames(Metadata(xenium_data))))

})

test_that("niche clustering", {

  data("xenium_data")

  ####

  # single assay

  ####

  # build niche assay

  xenium_data2 <- getSpatialNeighbors(xenium_data, radius = 15, method = "radius", verbose = FALSE)

  xenium_data2 <- getNicheAssay(xenium_data2, label = "clusters", graph.type = "radius")

  expect_equal(vrFeatureTypeNames(xenium_data2), c("RNA", "Niche"))

  xenium_data2 <- getNicheAssay(xenium_data2, label = "clusters", graph.type = "radius", new_feature_name = "Niche2")

  expect_equal(vrFeatureTypeNames(xenium_data2), c("RNA", "Niche", "Niche2"))

  expect_error(getNicheAssay(xenium_data2, label = "clusters1", graph.type = "radius"))

  # cluster niches

  vrMainFeatureType(xenium_data2) <- "Niche"

  xenium_data2 <- getClusters(xenium_data2, nclus = 3, method = "kmeans", label = "cluster_niches")

  expect_true("cluster_niches" %in% colnames(Metadata(xenium_data2)))

  expect_error(xenium_data2 <- getClusters(xenium_data2, nclus = 0, method = "kmeans", label = "cluster_niches"))

  expect_error(xenium_data2 <- getClusters(xenium_data2, nclus = 1.1, method = "kmeans", label = "cluster_niches"))

  expect_error(xenium_data2 <- getClusters(xenium_data2, nclus = -1, method = "kmeans", label = "cluster_niches"))

  expect_error(xenium_data2 <- getClusters(xenium_data2, nclus = c(1,2), method = "kmeans", label = "cluster_niches"))

  # clean

  rm(xenium_data2)

  ####

  # multiple assays

  ####

  xenium_data2 <- xenium_data

  xenium_data2$Sample <- "Sample2"

  xenium_data2 <- merge(xenium_data2, xenium_data, verbose = FALSE)

  xenium_data2 <- getSpatialNeighbors(xenium_data2, radius = 15, method = "radius", verbose = FALSE)

  xenium_data3 <- getNicheAssay(xenium_data2, label = "clusters", graph.type = "radius")

  metadata <- vrFeatureTypeNames(xenium_data3, assay = "all")

  expect_equal(metadata$Feature, c("RNA,Niche", "RNA,Niche"))

  xenium_data3 <- getNicheAssay(xenium_data2, assay = "Assay1", label = "clusters", graph.type = "radius")

  metadata <- vrFeatureTypeNames(xenium_data3, assay = "all")

  expect_equal(metadata$Feature, c("RNA,Niche", "RNA"))

  # clean

  rm(xenium_data2)

  rm(xenium_data3)

})

test_that("neighborhood analysis", {

  data("xenium_data")

  xenium_data <- getSpatialNeighbors(xenium_data, method = "delaunay", verbose = FALSE)

  results <- vrNeighbourhoodEnrichment(xenium_data, group.by = "clusters", graph.type = "delaunay")

  expect_error(results <- vrNeighbourhoodEnrichment(xenium_data, group.by = "clusters2", graph.type = "delaunay"))

})