tests/testthat/test_patchDetection.R
In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis
test_that("patchDetection function works", {
library(cytomapper)
data(pancreasSCE)
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
expect_true(is(cur_sce, "SingleCellExperiment"))
expect_true("patch_id" %in% names(colData(cur_sce)))
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
min_patch_size = 5))
expect_equal(unique(cur_sce$patch_id), c(NA, "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType %in% c("celltype_B", "celltype_A"),
colPairName = "expansion_interaction_graph"))
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType %in% c("celltype_B", "celltype_A", "celltype_C"),
colPairName = "expansion_interaction_graph"))
expect_equal(unique(cur_sce$patch_id), c("1", "2", "3"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id_2), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id_2")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 50, img_id = "ImageNb",
name = "patch_id"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1000, img_id = "ImageNb",
name = "patch_id"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c("3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 20, img_id = "ImageNb",
name = "patch_id",
min_patch_size = 5),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
cur_sce_2 <- pancreasSCE
cur_sce_2$X <- cur_sce_2$Pos_X
cur_sce_2$Y <- cur_sce_2$Pos_Y
cur_sce_2$Pos_X <- NULL
cur_sce_2$Pos_y <- NULL
expect_message(cur_sce <- patchDetection(cur_sce_2,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 30,
img_id = "ImageNb",
coords = c("X", "Y")),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "3", "4", "6", "7", "8"))
# Concave and convex
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 20, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1000, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c("3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
# Other graph constructors
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 1)
expect_error(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"),
regexp = "No interactions found.",
fixed = TRUE)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 10)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(39))))
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "knn", k = 3)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "knn_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(13))))
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "delaunay")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "delaunay_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(9))))
# Spatial Experiment
cur_spe <- SpatialExperiment:::.sce_to_spe(pancreasSCE, sample_id = as.character(pancreasSCE$ImageNb))
spatialCoords(cur_spe) <- as.matrix(colData(pancreasSCE)[,c("Pos_X", "Pos_Y")])
colData(cur_spe)[c("Pos_X", "Pos_Y")] <- NULL
cur_spe <- buildSpatialGraph(cur_spe, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_message(cur_spe_2 <- patchDetection(cur_spe,
patch_cells = cur_spe$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_spe_2$patch_id_2), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_spe_2, img_id = "ImageNb", node_color_by = "patch_id_2")
cur_spe_3 <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_message(cur_spe_3 <- patchDetection(cur_spe_3,
patch_cells = cur_spe_3$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(cur_spe_3$patch_id_2, cur_spe_2$patch_id_2)
plotSpatial(cur_spe_3, img_id = "ImageNb", node_color_by = "patch_id_2")
# Check that metadata is not duplicated
cur_sce <- pancreasSCE
metadata(cur_sce) <- list(test = c(1,2))
cur_sce <- patchDetection(cur_sce,
patch_cells = cur_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
expect_equal(length(metadata(cur_sce)), 1)
expect_equal(metadata(cur_sce), list(test = c(1, 2)))
int_metadata(cur_sce) <- list(version = "1.16.0")
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "knn", k = 5)
expect_equal(length(int_metadata(cur_sce)), 1)
expect_equal(int_metadata(cur_sce), list(version = "1.16.0"))
# Check for sparse graphs
cur_sce <- pancreasSCE
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "expansion", threshold = 10)
expect_silent(cur_sce <- patchDetection(cur_sce,
patch_cells = cur_sce$CellType == "celltype_C",
colPairName = "expansion_interaction_graph"))
# Error
expect_error(patchDetection("test"),
regexp = "'object' not of type 'SingleCellExperiment'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = "test"),
regexp = "'patch_cells' must all be logical.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = TRUE),
regexp = "Length of 'patch_cells' must match the number of cells in 'object'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = 1),
regexp = "'colPairName' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "test"),
regexp = "'colPairName' not in 'colPairNames(object)'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
min_patch_size = c(1,2)),
regexp = "'min_patch_size' must be a single numeric.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = 1),
regexp = "'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = c("test", "Pos_y")),
regexp = "'coords' not in colData(object).",
fixed = TRUE)
expect_error(patchDetection(cur_spe, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = c("test", "Pos_y")),
regexp = "'coords' not in spatialCoords(object).",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
name = c("test", "Pos_y")),
regexp = "'name' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = "test"),
regexp = "'expand_by' must be a single numeric.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
convex = "test"),
regexp = "'convex' must be a single logical.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10),
regexp = "'img_id' must be specified when patch expansion is performed.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = 1),
regexp = "'img_id' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "test"),
regexp = "'img_id' not in colData(object).",
fixed = TRUE)
})
test_that("patchDetection function works if cells are not ordered by image", {
library(cytomapper)
data(pancreasSCE)
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
pancreasSCE$index <- 1:ncol(pancreasSCE)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
set.seed(1234)
shuffled_sce <- pancreasSCE[,sample(ncol(pancreasSCE))]
cur_sce2 <- patchDetection(shuffled_sce,
patch_cells = shuffled_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(is.na(cur_sce2$patch_id[order(cur_sce2$index)]), is.na(cur_sce$patch_id[order(cur_sce$index)]))
expect_message(cur_sce <- patchDetection(pancreasSCE, img_id = "ImageNb",
patch_cells = pancreasSCE$CellType == "celltype_B",
expand_by = 10,
colPairName = "expansion_interaction_graph"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
set.seed(1234)
shuffled_sce <- pancreasSCE[,sample(ncol(pancreasSCE))]
cur_sce2 <- patchDetection(shuffled_sce, img_id = "ImageNb",
expand_by = 10,
patch_cells = shuffled_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(is.na(cur_sce2$patch_id[order(cur_sce2$index)]), is.na(cur_sce$patch_id[order(cur_sce$index)]))
})
BodenmillerGroup/imcRtools documentation built on Oct. 30, 2024, 12:19 p.m.
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test_that("patchDetection function works", {
library(cytomapper)
data(pancreasSCE)
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
expect_true(is(cur_sce, "SingleCellExperiment"))
expect_true("patch_id" %in% names(colData(cur_sce)))
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
min_patch_size = 5))
expect_equal(unique(cur_sce$patch_id), c(NA, "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType %in% c("celltype_B", "celltype_A"),
colPairName = "expansion_interaction_graph"))
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType %in% c("celltype_B", "celltype_A", "celltype_C"),
colPairName = "expansion_interaction_graph"))
expect_equal(unique(cur_sce$patch_id), c("1", "2", "3"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id_2), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id_2")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 50, img_id = "ImageNb",
name = "patch_id"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1000, img_id = "ImageNb",
name = "patch_id"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c("3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 20, img_id = "ImageNb",
name = "patch_id",
min_patch_size = 5),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
cur_sce_2 <- pancreasSCE
cur_sce_2$X <- cur_sce_2$Pos_X
cur_sce_2$Y <- cur_sce_2$Pos_Y
cur_sce_2$Pos_X <- NULL
cur_sce_2$Pos_y <- NULL
expect_message(cur_sce <- patchDetection(cur_sce_2,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 30,
img_id = "ImageNb",
coords = c("X", "Y")),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "3", "4", "6", "7", "8"))
# Concave and convex
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 20, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_message(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 1000, img_id = "ImageNb",
name = "patch_id",
convex = TRUE),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_sce$patch_id), c("3", "6", "7", "8"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
# Other graph constructors
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 1)
expect_error(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"),
regexp = "No interactions found.",
fixed = TRUE)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 10)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(39))))
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "knn", k = 3)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "knn_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(13))))
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "delaunay")
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "delaunay_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(unique(cur_sce$patch_id), c(NA, as.character(seq_len(9))))
# Spatial Experiment
cur_spe <- SpatialExperiment:::.sce_to_spe(pancreasSCE, sample_id = as.character(pancreasSCE$ImageNb))
spatialCoords(cur_spe) <- as.matrix(colData(pancreasSCE)[,c("Pos_X", "Pos_Y")])
colData(cur_spe)[c("Pos_X", "Pos_Y")] <- NULL
cur_spe <- buildSpatialGraph(cur_spe, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_message(cur_spe_2 <- patchDetection(cur_spe,
patch_cells = cur_spe$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(unique(cur_spe_2$patch_id_2), c(NA, "1", "2", "3", "4", "5", "6", "7", "8"))
plotSpatial(cur_spe_2, img_id = "ImageNb", node_color_by = "patch_id_2")
cur_spe_3 <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
expect_message(cur_spe_3 <- patchDetection(cur_spe_3,
patch_cells = cur_spe_3$CellType == "celltype_B",
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "ImageNb",
name = "patch_id_2"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
expect_equal(cur_spe_3$patch_id_2, cur_spe_2$patch_id_2)
plotSpatial(cur_spe_3, img_id = "ImageNb", node_color_by = "patch_id_2")
# Check that metadata is not duplicated
cur_sce <- pancreasSCE
metadata(cur_sce) <- list(test = c(1,2))
cur_sce <- patchDetection(cur_sce,
patch_cells = cur_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
expect_equal(length(metadata(cur_sce)), 1)
expect_equal(metadata(cur_sce), list(test = c(1, 2)))
int_metadata(cur_sce) <- list(version = "1.16.0")
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "knn", k = 5)
expect_equal(length(int_metadata(cur_sce)), 1)
expect_equal(int_metadata(cur_sce), list(version = "1.16.0"))
# Check for sparse graphs
cur_sce <- pancreasSCE
cur_sce <- buildSpatialGraph(cur_sce, img_id = "ImageNb",
type = "expansion", threshold = 10)
expect_silent(cur_sce <- patchDetection(cur_sce,
patch_cells = cur_sce$CellType == "celltype_C",
colPairName = "expansion_interaction_graph"))
# Error
expect_error(patchDetection("test"),
regexp = "'object' not of type 'SingleCellExperiment'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = "test"),
regexp = "'patch_cells' must all be logical.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = TRUE),
regexp = "Length of 'patch_cells' must match the number of cells in 'object'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = 1),
regexp = "'colPairName' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "test"),
regexp = "'colPairName' not in 'colPairNames(object)'.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
min_patch_size = c(1,2)),
regexp = "'min_patch_size' must be a single numeric.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = 1),
regexp = "'coords' must be a character vector of length 2.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = c("test", "Pos_y")),
regexp = "'coords' not in colData(object).",
fixed = TRUE)
expect_error(patchDetection(cur_spe, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
coords = c("test", "Pos_y")),
regexp = "'coords' not in spatialCoords(object).",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
name = c("test", "Pos_y")),
regexp = "'name' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = "test"),
regexp = "'expand_by' must be a single numeric.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
convex = "test"),
regexp = "'convex' must be a single logical.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10),
regexp = "'img_id' must be specified when patch expansion is performed.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = 1),
regexp = "'img_id' must be a single string.",
fixed = TRUE)
expect_error(patchDetection(pancreasSCE, patch_cells = pancreasSCE$Pattern,
colPairName = "expansion_interaction_graph",
expand_by = 10, img_id = "test"),
regexp = "'img_id' not in colData(object).",
fixed = TRUE)
})
test_that("patchDetection function works if cells are not ordered by image", {
library(cytomapper)
data(pancreasSCE)
cur_sce1 <- pancreasSCE[,pancreasSCE$ImageNb == 1]
cur_sce2 <- pancreasSCE[,pancreasSCE$ImageNb == 2]
cur_sce3 <- pancreasSCE[,pancreasSCE$ImageNb == 3]
cur_sce1$Pos_X <- cur_sce1$Pos_X - min(cur_sce1$Pos_X)
cur_sce1$Pos_Y <- cur_sce1$Pos_Y - min(cur_sce1$Pos_Y)
cur_sce2$Pos_X <- cur_sce2$Pos_X - min(cur_sce2$Pos_X)
cur_sce2$Pos_Y <- cur_sce2$Pos_Y - min(cur_sce2$Pos_Y)
cur_sce3$Pos_X <- cur_sce3$Pos_X - min(cur_sce3$Pos_X)
cur_sce3$Pos_Y <- cur_sce3$Pos_Y - min(cur_sce3$Pos_Y)
pancreasSCE <- cbind(cur_sce1, cur_sce2, cur_sce3)
pancreasSCE <- buildSpatialGraph(pancreasSCE, img_id = "ImageNb",
type = "expansion", threshold = 20)
pancreasSCE$index <- 1:ncol(pancreasSCE)
expect_silent(cur_sce <- patchDetection(pancreasSCE,
patch_cells = pancreasSCE$CellType == "celltype_B",
colPairName = "expansion_interaction_graph"))
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
set.seed(1234)
shuffled_sce <- pancreasSCE[,sample(ncol(pancreasSCE))]
cur_sce2 <- patchDetection(shuffled_sce,
patch_cells = shuffled_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(is.na(cur_sce2$patch_id[order(cur_sce2$index)]), is.na(cur_sce$patch_id[order(cur_sce$index)]))
expect_message(cur_sce <- patchDetection(pancreasSCE, img_id = "ImageNb",
patch_cells = pancreasSCE$CellType == "celltype_B",
expand_by = 10,
colPairName = "expansion_interaction_graph"),
regex = "The returned object is ordered by the 'ImageNb' entry.")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce, img_id = "ImageNb", node_color_by = "patch_id")
set.seed(1234)
shuffled_sce <- pancreasSCE[,sample(ncol(pancreasSCE))]
cur_sce2 <- patchDetection(shuffled_sce, img_id = "ImageNb",
expand_by = 10,
patch_cells = shuffled_sce$CellType == "celltype_B",
colPairName = "expansion_interaction_graph")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "CellType")
plotSpatial(cur_sce2, img_id = "ImageNb", node_color_by = "patch_id")
expect_equal(is.na(cur_sce2$patch_id[order(cur_sce2$index)]), is.na(cur_sce$patch_id[order(cur_sce$index)]))
})
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