test_that("spatial", {
# get data
data("xenium_data")
# profile neighbors, kNN
xenium_data <- getProfileNeighbors(xenium_data, method = "kNN", k = 10, data.type = "pca")
graphs <- vrGraph(xenium_data, graph.type = "kNN")
expect_true(inherits(graphs,"igraph"))
expect_true(length(igraph::E(graphs)) > 0)
xenium_data <- getClusters(xenium_data, graph = "kNN", label = "cluster_knn")
expect_true(is.numeric(unique(xenium_data$cluster_knn)))
# profile neighbors, SNN
xenium_data <- getProfileNeighbors(xenium_data, method = "SNN", k = 10, data.type = "pca")
graphs <- vrGraph(xenium_data, graph.type = "SNN")
expect_true(inherits(graphs,"igraph"))
expect_true(length(igraph::E(graphs)) > 0)
xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN")
expect_true(is.numeric(unique(xenium_data$cluster_SNN)))
# check parameters
expect_error(xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN", resolution = 0))
expect_error(xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN", resolution = c(0,1)))
expect_error(xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN", resolution = -0.5))
expect_error(xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN", resolution = 1, abundance_limit = 0))
expect_error(xenium_data <- getClusters(xenium_data, graph = "SNN", label = "cluster_SNN", resolution = 1, abundance_limit = 1.1))
# return
expect_equal(1,1L)
})