tests/testthat/test_read_steinbock.R
In BodenmillerGroup/imcRtools: Methods for imaging mass cytometry data analysis
test_that("read_steinbock function works", {
path <- system.file("extdata/mockData/steinbock", package = "imcRtools")
# SpatialExperiment
cur_spe <- read_steinbock(path)
expect_equal(colnames(cur_spe), paste0(cur_spe$sample_id, "_", cur_spe$ObjectNumber))
expect_s4_class(cur_spe, "SpatialExperiment")
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose",
"Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_spe)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909,
0.0909090909090909, 0.938306353308938, 0.181163804871695, 0,
0.142857142857143, 0.501448290688651, 1.00346943310329))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
cur_images <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE)
cur_images <- cur_images[order(cur_images$image, decreasing = FALSE),]
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
expect_equal(colPairNames(cur_spe), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood"))
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
# SingleCellExperiment
cur_sce <- read_steinbock(path, return_as = "sce")
expect_equal(colnames(cur_sce), paste0(cur_sce$sample_id, "_", cur_sce$ObjectNumber))
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_sce)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909,
0.0909090909090909, 0.938306353308938, 0.181163804871695, 0,
0.142857142857143, 0.501448290688651, 1.00346943310329))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood"))
for (i in unique(cur_sce$sample_id)) {
cur_dat <- cur_sce[,cur_sce$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
# Test other import settings
cur_spe <- read_steinbock(path, regionprops_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
expect_null(spatialCoordsNames(cur_spe))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_spe), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood"))
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
expect_equal(length(colPair(cur_spe)), 1674)
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
cur_sce <- read_steinbock(path, return_as = "sce", regionprops_folder = NULL)
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_equal(length(colPair(cur_sce)), 1674)
cur_spe <- read_steinbock(path, graphs_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_spe)), 0)
cur_sce <- read_steinbock(path, return_as = "sce", graphs_folder = NULL)
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_sce)), 0)
cur_spe <- read_steinbock(path, graphs_folder = NULL, regionprops_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
expect_null(spatialCoordsNames(cur_spe))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(cur_spe$ObjectNumber, cur_counts$Object)
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_spe)), 0)
cur_sce <- read_steinbock(path, return_as = "sce", graphs_folder = NULL, regionprops_folder = NULL)
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_sce)), 0)
cur_spe <- read_steinbock(path, pattern = "mockData2")
expect_equal(colnames(cur_spe), paste0(cur_spe$sample_id, "_", cur_spe$ObjectNumber))
expect_s4_class(cur_spe, "SpatialExperiment")
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 106))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2")
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_spe)[1:10], c(0.399655099572807, 0.0344827586206896, 4.64201253035973, 6.50705560733532,
3.57779644892133, 0.428760413080454, 0.0945868939161301, 1.56471130624413,
8.0167475938797, 1.46797196567059))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2")
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"))
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_spe), "neighborhood")
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
cur_images_2 <- cur_images[grepl("mockData2", cur_images$image),]
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(cur_images_2$width_px, cur_test$width_px)
expect_equal(cur_images_2$height_px, cur_test$height_px)
cur_sce <- read_steinbock(path, pattern = "mockData2", return_as = "sce")
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 106))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2")
cur_counts <- lapply(cur_files, readr::read_csv)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2")
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"))
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood"))
for (i in unique(cur_sce$sample_id)) {
cur_dat <- cur_sce[,cur_sce$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(cur_images_2$width_px, cur_test$width_px)
expect_equal(cur_images_2$height_px, cur_test$height_px)
cur_spe <- read_steinbock(path, panel = NULL)
expect_equal(length(rowData(cur_spe)), 0)
cur_sce <- read_steinbock(path, panel = NULL, return_as = "sce")
expect_equal(length(rowData(cur_sce)), 0)
cur_spe <- read_steinbock(path, extract_coords_from = c("area", "axis_major_length"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "centroid.0",
"centroid.1", "axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$`centroid.1`, cur_morph$`centroid-1`)
expect_equal(cur_spe$`centroid.0`, cur_morph$`centroid-0`)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$area)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$axis_major_length)
cur_sce <- read_steinbock(path, return_as = "sce", extract_coords_from = c("area", "axis_major_length"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "centroid.0",
"centroid.1", "axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$`centroid.0`, cur_morph$`centroid-0`)
expect_equal(cur_sce$`centroid.1`, cur_morph$`centroid-1`)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$area)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$axis_major_length)
# This test doesn't make sense anymore
#cur_spe <- read_steinbock(path, extract_names_from = "channel")
#expect_true(all(is.na(rowData(cur_spe)["Laminin",])))
#expect_equal(as.character(as.matrix(rowData(cur_spe)["Ag107",])),
# c("Ag107", "Ag107", "1", "1", NA, NA))
cur_spe <- read_steinbock(path, image_file = NULL)
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length", "axis_minor_length", "eccentricity"))
cur_sce <- read_steinbock(path, image_file = NULL, return_as = "sce")
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area",
"axis_major_length", "axis_minor_length", "eccentricity"))
cur_spe <- read_steinbock(path)
cur_images_file <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE)
cur_images_file <- cur_images_file[order(cur_images_file$image, decreasing = FALSE),]
cur_df <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(cur_images_file$image, paste0(cur_df$sample_id, ".tiff"))
expect_equal(cur_images_file$width_px, cur_df$width_px)
expect_equal(cur_images_file$height_px, cur_df$height_px)
cur_spe <- read_steinbock(path, extract_imagemetadata_from = c("recovered", "acquisition_description"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length", "axis_minor_length",
"eccentricity", "recovered", "acquisition_description"))
cur_df <- unique(colData(cur_spe)[,c("sample_id", "recovered", "acquisition_description")])
expect_equal(cur_images_file$image, paste0(cur_df$sample_id, ".tiff"))
expect_equal(cur_images_file$recovered, cur_df$recovered)
expect_equal(cur_images_file$acquisition_description, cur_df$acquisition_description)
# Parallelisation
#cur_spe <- read_steinbock(path, BPPARAM = BiocParallel::bpparam())
# Error
expect_error(cur_spe <- read_steinbock(path = "test"),
"'path' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path = c("test", "test2")),
"'path' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path = 1),
"'path' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = NULL),
"'intensities_folder' must be specified.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = "test"),
"'intensities_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = c("test", "test2")),
"'intensities_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = 1),
"'intensities_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = "test"),
"'regionprops_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = c("test", "test2")),
"'regionprops_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = 1),
"'regionprops_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = "test"),
"'graphs_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = c("test", "test2")),
"'graphs_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = 1),
"'graphs_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, pattern = "test"),
"No files were read in.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = "test"),
"'extract_cellid_from' not in intensities files.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = c("test", "test2")),
"'extract_cellid_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = 1),
"'extract_cellid_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_coords_from = "test"),
"'coords' not in regionprops files.",
fixed = TRUE)
expect_silent(cur_spe <- read_steinbock(path, extract_coords_from = "test", regionprops_folder = NULL))
expect_error(cur_spe <- read_steinbock(path, extract_coords_from = 1),
"'extract_coords_from' must be characters.",
fixed = TRUE)
expect_warning(cur_spe <- read_steinbock(path, panel = "test"),
"'panel_file' does not exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, panel = c("test", "test2")),
"'panel_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, panel = 1),
"'panel_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = "test"),
"'extract_names_from' not in panel file.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = c("test", "test2")),
"'extract_names_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = 1),
"'extract_names_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, image_file = 1),
"'image_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, image_file = "test"),
"'image_file' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_imagemetadata_from = 1),
"'extract_imagemetadata_from' should only contain characters.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_imagemetadata_from = c(1, "test")),
"'extract_imagemetadata_from' not in images file.",
fixed = TRUE)
})
test_that("read_steinbock function works when files are missing", {
skip_on_os(os = "windows")
path <- system.file("extdata/mockData/steinbock", package = "imcRtools")
# Move files to tmp location
cur_path <- tempdir()
file.copy(path, cur_path, recursive = TRUE)
# Remove regionprobs folder
file.remove(list.files(paste0(cur_path, "/steinbock/regionprops"),
full.names = TRUE))
expect_error(cur_spe <- read_steinbock(paste0(cur_path, "/steinbock/")),
"File names in 'intensities' and 'regionprops' do not match.",
fixed = TRUE)
# Remove graphs folder
file.remove(list.files(paste0(cur_path, "/steinbock/neighbors"),
full.names = TRUE))
expect_error(cur_spe <- read_steinbock(paste0(cur_path, "/steinbock/")),
"File names in 'intensities' and 'neighbors' do not match.",
fixed = TRUE)
})
BodenmillerGroup/imcRtools documentation built on July 1, 2024, 5:15 p.m.
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test_that("read_steinbock function works", {
path <- system.file("extdata/mockData/steinbock", package = "imcRtools")
# SpatialExperiment
cur_spe <- read_steinbock(path)
expect_equal(colnames(cur_spe), paste0(cur_spe$sample_id, "_", cur_spe$ObjectNumber))
expect_s4_class(cur_spe, "SpatialExperiment")
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose",
"Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_spe)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909,
0.0909090909090909, 0.938306353308938, 0.181163804871695, 0,
0.142857142857143, 0.501448290688651, 1.00346943310329))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
cur_images <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE)
cur_images <- cur_images[order(cur_images$image, decreasing = FALSE),]
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
expect_equal(colPairNames(cur_spe), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood"))
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
# SingleCellExperiment
cur_sce <- read_steinbock(path, return_as = "sce")
expect_equal(colnames(cur_sce), paste0(cur_sce$sample_id, "_", cur_sce$ObjectNumber))
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_sce)[1:10], c(0.0909090909090909, 0.181818181818182, 0.0909090909090909,
0.0909090909090909, 0.938306353308938, 0.181163804871695, 0,
0.142857142857143, 0.501448290688651, 1.00346943310329))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood"))
for (i in unique(cur_sce$sample_id)) {
cur_dat <- cur_sce[,cur_sce$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
# Test other import settings
cur_spe <- read_steinbock(path, regionprops_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
expect_null(spatialCoordsNames(cur_spe))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_spe), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_spe, "neighborhood"))
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
expect_equal(length(colPair(cur_spe)), 1674)
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
cur_sce <- read_steinbock(path, return_as = "sce", regionprops_folder = NULL)
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_equal(length(colPair(cur_sce)), 1674)
cur_spe <- read_steinbock(path, graphs_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_spe)), 0)
cur_sce <- read_steinbock(path, return_as = "sce", graphs_folder = NULL)
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_sce)), 0)
cur_spe <- read_steinbock(path, graphs_folder = NULL, regionprops_folder = NULL)
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 404))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
expect_null(spatialCoordsNames(cur_spe))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(cur_spe$ObjectNumber, cur_counts$Object)
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images$image), cur_test$sample_id)
expect_equal(cur_images$width_px, cur_test$width_px)
expect_equal(cur_images$height_px, cur_test$height_px)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_spe)), 0)
cur_sce <- read_steinbock(path, return_as = "sce", graphs_folder = NULL, regionprops_folder = NULL)
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 404))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE)
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_panel <- readr::read_csv(file.path(path, "panel.csv"), show_col_types = FALSE)
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(length(colPairs(cur_sce)), 0)
cur_spe <- read_steinbock(path, pattern = "mockData2")
expect_equal(colnames(cur_spe), paste0(cur_spe$sample_id, "_", cur_spe$ObjectNumber))
expect_s4_class(cur_spe, "SpatialExperiment")
expect_equal(rownames(cur_spe), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_spe), "counts")
expect_equal(dim(cur_spe), c(5, 106))
expect_equal(names(rowData(cur_spe)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2")
cur_counts <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_spe)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
expect_equal(counts(cur_spe)[1:10], c(0.399655099572807, 0.0344827586206896, 4.64201253035973, 6.50705560733532,
3.57779644892133, 0.428760413080454, 0.0945868939161301, 1.56471130624413,
8.0167475938797, 1.46797196567059))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2")
cur_morph <- lapply(cur_files, readr::read_csv, show_col_types = FALSE)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$area, cur_morph$area)
expect_equal(cur_spe$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$`centroid-1`)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"))
expect_equal(rowData(cur_spe)$name, cur_panel$name)
expect_equal(rowData(cur_spe)$channel, cur_panel$channel)
expect_equal(rowData(cur_spe)$keep, cur_panel$keep)
expect_equal(rowData(cur_spe)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_spe)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_spe)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_spe), "neighborhood")
for (i in unique(cur_spe$sample_id)) {
cur_dat <- cur_spe[,cur_spe$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
cur_images_2 <- cur_images[grepl("mockData2", cur_images$image),]
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(cur_images_2$width_px, cur_test$width_px)
expect_equal(cur_images_2$height_px, cur_test$height_px)
cur_sce <- read_steinbock(path, pattern = "mockData2", return_as = "sce")
expect_s4_class(cur_sce, "SingleCellExperiment")
expect_equal(rownames(cur_sce), c("Ag107", "Cytokeratin 5", "Laminin",
"YBX1", "H3K27Ac"))
expect_equal(assayNames(cur_sce), "counts")
expect_equal(dim(cur_sce), c(5, 106))
expect_equal(names(rowData(cur_sce)),
c("channel", "name", "keep", "ilastik", "deepcell", "cellpose", "Tube.Number"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X",
"Pos_Y", "area",
"axis_major_length",
"axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "intensities"), full.names = TRUE, pattern = "mockData2")
cur_counts <- lapply(cur_files, readr::read_csv)
cur_counts <- do.call("rbind", cur_counts)
test1 <- counts(cur_sce)
colnames(test1) <- NULL
expect_equal(test1, t(cur_counts[,-1]))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE, pattern = "mockData2")
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$area, cur_morph$area)
expect_equal(cur_sce$axis_major_length, cur_morph$axis_major_length)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$`centroid-1`)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$`centroid-0`)
cur_panel <- readr::read_csv(file.path(path, "panel.csv"))
expect_equal(rowData(cur_sce)$name, cur_panel$name)
expect_equal(rowData(cur_sce)$channel, cur_panel$channel)
expect_equal(rowData(cur_sce)$keep, cur_panel$keep)
expect_equal(rowData(cur_sce)$deepcell, cur_panel$deepcell)
expect_equal(rowData(cur_sce)$ilastik, cur_panel$ilastik)
expect_equal(rowData(cur_sce)$Tube.Number, cur_panel$`Tube Number`)
expect_equal(colPairNames(cur_sce), "neighborhood")
expect_silent(cur_graphs <- colPair(cur_sce, "neighborhood"))
for (i in unique(cur_sce$sample_id)) {
cur_dat <- cur_sce[,cur_sce$sample_id == i]
cur_test <- readr::read_csv(file.path(path, "neighbors", paste0(i, ".csv")), show_col_types = FALSE)
expect_equal(cur_test$Object, from(colPair(cur_dat, "neighborhood")))
expect_equal(cur_test$Neighbor, to(colPair(cur_dat, "neighborhood")))
}
cur_test <- unique(colData(cur_sce)[,c("sample_id", "width_px", "height_px")])
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(sub(".tiff$", "", cur_images_2$image), cur_test$sample_id)
expect_equal(cur_images_2$width_px, cur_test$width_px)
expect_equal(cur_images_2$height_px, cur_test$height_px)
cur_spe <- read_steinbock(path, panel = NULL)
expect_equal(length(rowData(cur_spe)), 0)
cur_sce <- read_steinbock(path, panel = NULL, return_as = "sce")
expect_equal(length(rowData(cur_sce)), 0)
cur_spe <- read_steinbock(path, extract_coords_from = c("area", "axis_major_length"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "centroid.0",
"centroid.1", "axis_minor_length", "eccentricity",
"width_px", "height_px"))
expect_equal(spatialCoordsNames(cur_spe), c("Pos_X", "Pos_Y"))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_spe$`centroid.1`, cur_morph$`centroid-1`)
expect_equal(cur_spe$`centroid.0`, cur_morph$`centroid-0`)
expect_equal(cur_spe$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_spe$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(spatialCoords(cur_spe)[,1]), cur_morph$area)
expect_equal(as.numeric(spatialCoords(cur_spe)[,2]), cur_morph$axis_major_length)
cur_sce <- read_steinbock(path, return_as = "sce", extract_coords_from = c("area", "axis_major_length"))
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "centroid.0",
"centroid.1", "axis_minor_length", "eccentricity",
"width_px", "height_px"))
cur_files <- list.files(file.path(path, "regionprops"), full.names = TRUE)
cur_morph <- lapply(cur_files, readr::read_csv)
cur_morph <- do.call("rbind", cur_morph)
expect_equal(cur_sce$`centroid.0`, cur_morph$`centroid-0`)
expect_equal(cur_sce$`centroid.1`, cur_morph$`centroid-1`)
expect_equal(cur_sce$axis_minor_length, cur_morph$axis_minor_length)
expect_equal(cur_sce$eccentricity, cur_morph$eccentricity)
expect_equal(as.numeric(cur_sce$Pos_X), cur_morph$area)
expect_equal(as.numeric(cur_sce$Pos_Y), cur_morph$axis_major_length)
# This test doesn't make sense anymore
#cur_spe <- read_steinbock(path, extract_names_from = "channel")
#expect_true(all(is.na(rowData(cur_spe)["Laminin",])))
#expect_equal(as.character(as.matrix(rowData(cur_spe)["Ag107",])),
# c("Ag107", "Ag107", "1", "1", NA, NA))
cur_spe <- read_steinbock(path, image_file = NULL)
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length", "axis_minor_length", "eccentricity"))
cur_sce <- read_steinbock(path, image_file = NULL, return_as = "sce")
expect_equal(names(colData(cur_sce)), c("sample_id", "ObjectNumber", "Pos_X", "Pos_Y", "area",
"axis_major_length", "axis_minor_length", "eccentricity"))
cur_spe <- read_steinbock(path)
cur_images_file <- readr::read_csv(file.path(path, "images.csv"), show_col_types = FALSE)
cur_images_file <- cur_images_file[order(cur_images_file$image, decreasing = FALSE),]
cur_df <- unique(colData(cur_spe)[,c("sample_id", "width_px", "height_px")])
expect_equal(cur_images_file$image, paste0(cur_df$sample_id, ".tiff"))
expect_equal(cur_images_file$width_px, cur_df$width_px)
expect_equal(cur_images_file$height_px, cur_df$height_px)
cur_spe <- read_steinbock(path, extract_imagemetadata_from = c("recovered", "acquisition_description"))
expect_equal(names(colData(cur_spe)), c("sample_id", "ObjectNumber", "area",
"axis_major_length", "axis_minor_length",
"eccentricity", "recovered", "acquisition_description"))
cur_df <- unique(colData(cur_spe)[,c("sample_id", "recovered", "acquisition_description")])
expect_equal(cur_images_file$image, paste0(cur_df$sample_id, ".tiff"))
expect_equal(cur_images_file$recovered, cur_df$recovered)
expect_equal(cur_images_file$acquisition_description, cur_df$acquisition_description)
# Parallelisation
#cur_spe <- read_steinbock(path, BPPARAM = BiocParallel::bpparam())
# Error
expect_error(cur_spe <- read_steinbock(path = "test"),
"'path' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path = c("test", "test2")),
"'path' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path = 1),
"'path' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = NULL),
"'intensities_folder' must be specified.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = "test"),
"'intensities_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = c("test", "test2")),
"'intensities_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, intensities_folder = 1),
"'intensities_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = "test"),
"'regionprops_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = c("test", "test2")),
"'regionprops_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, regionprops_folder = 1),
"'regionprops_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = "test"),
"'graphs_folder' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = c("test", "test2")),
"'graphs_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, graphs_folder = 1),
"'graphs_folder' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, pattern = "test"),
"No files were read in.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = "test"),
"'extract_cellid_from' not in intensities files.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = c("test", "test2")),
"'extract_cellid_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_cellid_from = 1),
"'extract_cellid_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_coords_from = "test"),
"'coords' not in regionprops files.",
fixed = TRUE)
expect_silent(cur_spe <- read_steinbock(path, extract_coords_from = "test", regionprops_folder = NULL))
expect_error(cur_spe <- read_steinbock(path, extract_coords_from = 1),
"'extract_coords_from' must be characters.",
fixed = TRUE)
expect_warning(cur_spe <- read_steinbock(path, panel = "test"),
"'panel_file' does not exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, panel = c("test", "test2")),
"'panel_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, panel = 1),
"'panel_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = "test"),
"'extract_names_from' not in panel file.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = c("test", "test2")),
"'extract_names_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_names_from = 1),
"'extract_names_from' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, image_file = 1),
"'image_file' must be a single string.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, image_file = "test"),
"'image_file' doesn't exist.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_imagemetadata_from = 1),
"'extract_imagemetadata_from' should only contain characters.",
fixed = TRUE)
expect_error(cur_spe <- read_steinbock(path, extract_imagemetadata_from = c(1, "test")),
"'extract_imagemetadata_from' not in images file.",
fixed = TRUE)
})
test_that("read_steinbock function works when files are missing", {
skip_on_os(os = "windows")
path <- system.file("extdata/mockData/steinbock", package = "imcRtools")
# Move files to tmp location
cur_path <- tempdir()
file.copy(path, cur_path, recursive = TRUE)
# Remove regionprobs folder
file.remove(list.files(paste0(cur_path, "/steinbock/regionprops"),
full.names = TRUE))
expect_error(cur_spe <- read_steinbock(paste0(cur_path, "/steinbock/")),
"File names in 'intensities' and 'regionprops' do not match.",
fixed = TRUE)
# Remove graphs folder
file.remove(list.files(paste0(cur_path, "/steinbock/neighbors"),
full.names = TRUE))
expect_error(cur_spe <- read_steinbock(paste0(cur_path, "/steinbock/")),
"File names in 'intensities' and 'neighbors' do not match.",
fixed = TRUE)
})
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