tests/testthat/test_minDistToCells.R

In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis

test_that("minDistToCells works",{
  data("pancreasSCE")
  
  # works when cell types present and with negative distances returned
  expect_message(cur_sce <- minDistToCells(object = pancreasSCE,
                 x_cells = pancreasSCE$CellType == "celltype_B",
                 coords = c("Pos_X","Pos_Y"),
                 img_id = "ImageName"), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_s4_class(cur_sce , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce)))
  expect_true(class(cur_sce$distToCells) == "numeric")
  expect_true(min(cur_sce$distToCells) < 0)
  
  # works on cell types when present and no negative distances returned
  expect_message(cur_sce_2 <- minDistToCells(object = pancreasSCE,
                                          x_cells = pancreasSCE$CellType == "celltype_B",
                                          coords = c("Pos_X","Pos_Y"),
                                          img_id = "ImageName",
                                          return_neg = FALSE), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_true(is(cur_sce_2, "SingleCellExperiment"))
  expect_s4_class(cur_sce_2 , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce_2)))
  expect_true(class(cur_sce_2$distToCells) == "numeric")
  expect_true(min(cur_sce_2$distToCells) == 0)
  
  expect_equal(cur_sce[,cur_sce$distToCells > 0]$distToCells,cur_sce_2[,cur_sce_2$distToCells > 0]$distToCells)
  
  expect_equal(length(cur_sce[,cur_sce$distToCells < 0]),length(cur_sce_2[,cur_sce_2$distToCells == 0]))

  # works on cell types when not present in some image and with negative distances returned
  expect_message(cur_sce_3 <- minDistToCells(object = pancreasSCE,
                                          x_cells = pancreasSCE$CellType == "celltype_A",
                                          coords = c("Pos_X","Pos_Y"),
                                          img_id = "ImageName"), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_true(is(cur_sce_3, "SingleCellExperiment"))
  expect_s4_class(cur_sce_3 , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce_3)))
  expect_true(is(cur_sce_3$distToCells, "numeric"))
  
  expect_true(any(is.na(cur_sce_3$distToCells)))
  expect_true(all(is.na(cur_sce_3[,cur_sce_3$ImageName == "J02_imc.tiff"]$distToCells)))
  expect_true(min(cur_sce_3[,!is.na(cur_sce_3$distToCells)]$distToCells)<0)
  
  expect_equal(length(cur_sce_3[,cur_sce_3$ImageName == "J02_imc.tiff"]$CellNb),sum(is.na(cur_sce_3$distToCells)))
  
  # works on cell types when not present in some images and no negative distances returned
  expect_message(cur_sce_4 <- minDistToCells(object = pancreasSCE,
                                            x_cells = pancreasSCE$CellType == "celltype_A",
                                            coords = c("Pos_X","Pos_Y"),
                                            img_id = "ImageName",
                                            return_neg = FALSE), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_true(is(cur_sce_4, "SingleCellExperiment"))
  expect_s4_class(cur_sce_4 , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce_4)))
  expect_true(is(cur_sce_4$distToCells, "numeric"))
  
  expect_true(any(is.na(cur_sce_4$distToCells)))
  expect_true(all(is.na(cur_sce_4[,cur_sce_4$ImageName == "J02_imc.tiff"]$distToCells)))
  expect_true(min(cur_sce_4[,!is.na(cur_sce_4$distToCells)]$distToCells) == 0)
  
  expect_equal(length(cur_sce_4[,cur_sce_4$ImageName == "J02_imc.tiff"]$CellNb),sum(is.na(cur_sce_4$distToCells)))

  # 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_1 <- minDistToCells(cur_spe,
                              x_cells = cur_spe$CellType == "celltype_B",
                              coords = c("Pos_X","Pos_Y"),
                              img_id = "ImageName")
  
  expect_true(is(cur_spe_1, "SingleCellExperiment"))
  expect_s4_class(cur_spe_1 , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_spe_1)))
  expect_true(class(cur_spe_1$distToCells) == "numeric")
  expect_true(min(cur_spe_1$distToCells) < 0)
  
  # works on cell types when present and no negative distances returned
  expect_message(cur_spe_2 <- minDistToCells(object = pancreasSCE,
                                            x_cells = pancreasSCE$CellType == "celltype_B",
                                            coords = c("Pos_X","Pos_Y"),
                                            img_id = "ImageName",
                                            return_neg = FALSE), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_true(is(cur_spe_2, "SingleCellExperiment"))
  expect_s4_class(cur_spe_2 , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_spe_2)))
  expect_true(class(cur_spe_2$distToCells) == "numeric")
  expect_true(min(cur_spe_2$distToCells) == 0)
  
  expect_equal(cur_spe_1[,cur_spe_1$distToCells > 0]$distToCells,cur_spe_2[,cur_spe_2$distToCells > 0]$distToCells)
  
  expect_equal(length(cur_spe_1[,cur_spe_1$distToCells < 0]),length(cur_spe_2[,cur_spe_2$distToCells == 0]))
  
  # compare results from SingleCellExperiment and SpatialExperiment
  expect_equal(cur_sce$distToCells,cur_spe_1$distToCells)
  
  expect_equal(cur_sce_2$distToCells,cur_spe_2$distToCells)
  
  # Works when all cells of an image belog to one batch
  expect_message(cur_sce <- minDistToCells(object = pancreasSCE,
                                          x_cells = pancreasSCE$ImageName == "J02_imc.tiff",
                                          coords = c("Pos_X","Pos_Y"),
                                          img_id = "ImageName"), regexp = "The returned object is ordered by the 'ImageName' entry.")
  
  expect_s4_class(cur_sce , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce)))
  expect_true(all(is.na(cur_sce$distToCells)))
  
  cur_sce$CellType[cur_sce$ImageName == "J02_imc.tiff"] <- "celltype_A"
  expect_message(cur_sce <- minDistToCells(object = cur_sce,
                                          x_cells = cur_sce$CellType == "celltype_A",
                                          coords = c("Pos_X","Pos_Y"),
                                          img_id = "ImageName"), regexp = "The returned object is ordered by the 'ImageName' entry.")
  expect_s4_class(cur_sce , class = "SingleCellExperiment")
  expect_true("distToCells" %in% names(colData(cur_sce)))
  expect_true(all(is.na(cur_sce$distToCells[cur_sce$ImageName == "J02_imc.tiff"])))
  expect_true(all(!is.na(cur_sce$distToCells[cur_sce$ImageName != "J02_imc.tiff"])))
  
  # Error
  expect_error(cur_sce_4 <- minDistToCells(object = pancreasSCE[,pancreasSCE$ImageName == "J02_imc.tiff"],
                                            x_cells = pancreasSCE$CellType == "celltype_A",
                                            coords = c("Pos_X","Pos_Y"),
                                            img_id = "ImageName",
                                            return_neg = FALSE),
                regexp = "Length of 'x_cells' must match the number of cells in 'object'.")
  
  expect_error(minDistToCells(object = "test"),
               regexp = "'object' not of type 'SingleCellExperiment'.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = "test"),
               regexp = "'x_cells' must all be logical.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = TRUE),
               regexp = "Length of 'x_cells' must match the number of cells in 'object'.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = TRUE),
               regexp = "'name' must be a single string.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = 1),
               regexp = "'name' must be a single string.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c(1,2)),
               regexp = "'coords' must be a character vector of length 2.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("A","B")),
               regexp = "'coords' not in colData(object).",
               fixed = TRUE)
  expect_error(minDistToCells(cur_spe, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("A","B")),
               regexp = "'coords' not in spatialCoords(object).",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("Pos_X","Pos_Y"),img_id = 1),
               regexp = "'img_id' must be a single string.",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("Pos_X","Pos_Y"),img_id = "test"),
               regexp = "'img_id' not in colData(object).",
               fixed = TRUE)
  expect_error(minDistToCells(pancreasSCE, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("Pos_X","Pos_Y"),
                              img_id = "ImageName",return_neg = 1),
               regexp = "'return_neg' is not of type logical.",
               fixed = TRUE)
  expect_error(minDistToCells(cur_spe, x_cells = pancreasSCE$CellType ==  "celltype_B",name = "test",coords = c("Pos_1","Pos_Y")),
               regexp = "'coords' not in spatialCoords(object).",
               fixed = TRUE)
})