# packages
skip_if_not_installed("rhdf5")
skip_if_not_installed("pizzarr")
skip_if_not_installed("HDF5Array")
skip_if_not_installed("HDF5DataFrame")
skip_if_not_installed("ZarrArray")
skip_if_not_installed("ZarrDataFrame")
skip_if_not_installed("ImageArray")
skip_if_not_installed("BPCells")
# create dir
dir.create(td <- tempfile())
output_zarr <- paste0(td, "/xenium_data_zarr_test")
output_h5ad <- paste0(td, "/xenium_data_h5_test")
output_h5ad_2 <- paste0(td, "/xenium_data_h5_test")
output_h5ad_merged <- paste0(td, "/xenium_data_merged_h5_test")
test_that("save and load on disk", {
# get data
data("xenium_data")
# HDF5
xenium_data2 <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
xenium_data2 <- loadVoltRon(dir = output_h5ad)
# TODO: output zarr problem with path
# zarr
xenium_data2 <- saveVoltRon(xenium_data,
output = output_zarr,
format = "ZarrVoltRon",
replace = TRUE,
verbose = FALSE)
xenium_data2 <- loadVoltRon(dir = output_zarr)
# remove files
unlink(output_h5ad, recursive = TRUE)
unlink(output_zarr, recursive = TRUE)
expect_equal(1,1L)
})
test_that("double write and merging", {
# get data
data("visium_data")
data("xenium_data")
# TODO: output zarr problem with path
# write merged data
xenium_data2 <- xenium_data
xenium_data2$Sample <- "XeniumR2"
xenium_data2 <- merge(xenium_data, xenium_data2, verbose = FALSE)
xenium_data3 <- saveVoltRon(xenium_data2,
output = output_zarr,
format = "ZarrVoltRon",
replace = TRUE,
verbose = FALSE)
# merged ondisk data
xenium_data_disk <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
xenium_data2 <- xenium_data
xenium_data2$Sample <- "XeniumR2"
xenium_data2_disk <- saveVoltRon(xenium_data2,
output = output_h5ad_2,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
xenium_data_merged <- merge(xenium_data_disk, xenium_data2_disk, verbose = FALSE)
xenium_data_merged_disk <- saveVoltRon(xenium_data_merged,
output = output_h5ad_merged,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
# remove files
unlink(output_h5ad, recursive = TRUE)
unlink(output_h5ad_2, recursive = TRUE)
unlink(output_h5ad_merged, recursive = TRUE)
unlink(output_zarr, recursive = TRUE)
expect_equal(1,1L)
})
test_that("subsetting", {
# get data
data("xenium_data")
# HDF5
xenium_data2 <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
# by spatialpoints
spatpoints <- vrSpatialPoints(xenium_data2)[1:30]
xenium_data2_subset <- subset(xenium_data2, spatialpoints = spatpoints)
expect_equal(vrSpatialPoints(xenium_data2_subset), spatpoints)
# visualize
vrSpatialPlot(xenium_data2_subset)
vrSpatialFeaturePlot(xenium_data2_subset, features = "KRT15")
# by image
xenium_data2_subset <- subset(xenium_data2, image = "290x202+98+17")
expect_equal(length(vrSpatialPoints(xenium_data2_subset)), 392)
expect_equal(is(vrImages(xenium_data2_subset)), "magick-image")
expect_equal(is(vrImages(xenium_data2_subset, as.raster = TRUE)), "Image_Array")
# visualize
vrSpatialPlot(xenium_data2_subset)
vrSpatialFeaturePlot(xenium_data2_subset, features = "KRT15")
# remove files
unlink(output_h5ad, recursive = TRUE)
expect_equal(1,1L)
})
test_that("metadata", {
# get data
data("xenium_data")
# HDF5
xenium_data2 <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
# add column to metadata
xenium_data2$new_column <- vrSpatialPoints(xenium_data2)
# save updated metadata
xenium_data2 <- saveVoltRon(xenium_data2, verbose = FALSE)
meta.data <- Metadata(xenium_data2)
expect_true(is(meta.data@listData[["new_column"]], "HDF5ColumnVector"))
# load after update
xenium_data2 <- loadVoltRon(output_h5ad)
meta.data <- Metadata(xenium_data2)
expect_true(is(meta.data@listData[["new_column"]], "HDF5ColumnVector"))
# remove files
unlink(output_h5ad, recursive = TRUE)
expect_equal(1,1L)
})
test_that("embeddings", {
# get data
data("xenium_data")
# HDF5
xenium_data2 <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
xenium_data2 <- getPCA(xenium_data2, features = vrFeatures(xenium_data2), type = "pca_key")
# check embeddings
emb <- vrEmbeddings(xenium_data2, type = "pca_key")
expect_true(all(dim(emb) > 1))
expect_true(all(vrEmbeddingNames(xenium_data2) == c("pca", "umap", "pca_key")))
# remove files
unlink(output_h5ad, recursive = TRUE)
expect_equal(1,1L)
})
test_that("visualization", {
# get data
data("visium_data")
# HDF5
visium_data2 <- saveVoltRon(visium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
# check spatial plots
vrSpatialPlot(visium_data2, group.by = "Sample")
vrSpatialFeaturePlot(visium_data2, features = "Count")
# check multilayer spatial plots
data("merged_object")
merged_object2 <- saveVoltRon(merged_object,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
vrSpatialPlot(merged_object2, plot.segments = FALSE, n.tile = 100) |>
addSpatialLayer(merged_object2, assay = "Assay3", group.by = "Sample", alpha = 0.4, colors = list(Block = "blue"))
vrSpatialPlot(merged_object2, plot.segments = TRUE, n.tile = 100) |>
addSpatialLayer(merged_object2, assay = "Assay3", group.by = "Sample", alpha = 0.4, colors = list(Block = "blue"))
vrSpatialPlot(merged_object2, assay = "Assay2", group.by = "gene", alpha = 1, colors = list(KRT15 = "blue", KRT14 = "green"), n.tile = 100) |>
addSpatialLayer(merged_object2, assay = "Assay3", group.by = "Sample", alpha = 0.4, colors = list(Block = "blue"))
# remove files
unlink(output_h5ad, recursive = TRUE)
expect_equal(1,1L)
})
test_that("neighbors", {
# get data
data("xenium_data")
# HDF5
xenium_data2 <- saveVoltRon(xenium_data,
output = output_h5ad,
format = "HDF5VoltRon",
replace = TRUE,
verbose = FALSE)
# spatial neighbors, delaunay
xenium_data2 <- getSpatialNeighbors(xenium_data2, method = "delaunay")
graphs <- vrGraph(xenium_data2, graph.type = "delaunay")
expect_true(inherits(graphs,"igraph"))
expect_true(length(igraph::E(graphs)) > 0)
# profile neighbors, kNN
xenium_data2 <- getProfileNeighbors(xenium_data2, method = "kNN", k = 10, data.type = "pca")
graphs <- vrGraph(xenium_data2, graph.type = "kNN")
expect_true(inherits(graphs,"igraph"))
expect_true(length(igraph::E(graphs)) > 0)
xenium_data2 <- getClusters(xenium_data2, graph = "kNN", label = "cluster_knn")
expect_true(is.numeric(unique(xenium_data2$cluster_knn)))
# update metadata
xenium_data2 <- saveVoltRon(xenium_data2, verbose = FALSE)
meta.data <- Metadata(xenium_data2)
expect_true(is(meta.data@listData[["cluster_knn"]], "HDF5ColumnVector"))
# load after update
xenium_data2 <- loadVoltRon(output_h5ad)
meta.data <- Metadata(xenium_data2)
expect_true(is(meta.data@listData[["cluster_knn"]], "HDF5ColumnVector"))
# remove files
unlink(output_h5ad, recursive = TRUE)
expect_equal(1,1L)
})
Datasets
Models
