CI
b1ffb24eb9
Build pipeline: openpipelines-bio.openpipeline-spatial.build-main-vdjx9
Source commit: 226d7de695
Source message: deploy: 46b97b56724d241439f09d3748315a26f03a300d
112 lines
2.8 KiB
R
112 lines
2.8 KiB
R
library(testthat, warn.conflicts = FALSE)
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library(SpatialExperimentIO)
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library(SpatialExperiment)
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## VIASH START
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meta <- list(
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executable = "./from_xenium_to_spatialexperiment",
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resources_dir = "resources_test/xenium",
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name = "from_xenium_to_spatial_experiment"
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)
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## VIASH END
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cat("> Checking simple execution\n")
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spe <- paste0(
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meta[["resources_dir"]],
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"/xenium_tiny"
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)
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out_rds <- "output.rds"
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cat("> Running ", meta[["name"]], "\n", sep = "")
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out <- processx::run(
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meta[["executable"]],
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c(
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"--input", spe,
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"--output", out_rds
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)
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)
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cat("> Checking whether output file exists\n")
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expect_equal(out$status, 0)
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expect_true(file.exists(out_rds))
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cat("> Reading output file\n")
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obj <- readRDS(file = out_rds)
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cat("> Checking whether Seurat object is in the right format\n")
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# Object type
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expect_is(obj, "SpatialExperiment")
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# Assay structure
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expect_equal(names(slot(obj, "assays")), "counts")
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# Spatial coordinates
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expect_equal(spatialCoordsNames(obj), c("x_centroid", "y_centroid"))
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# Alternative experiments
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expect_equal(
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altExpNames(obj),
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c("NegControlProbe", "UnassignedCodeword", "NegControlCodeword")
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)
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# Metadata components
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metadata_components <- c(
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"experiment.xenium", "transcripts", "cell_boundaries", "nucleus_boundaries"
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)
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expect_named(
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metadata(obj),
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metadata_components,
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ignore.order = TRUE
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)
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# Parquet paths
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parquet_components <- c("transcripts", "cell_boundaries", "nucleus_boundaries")
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for (component in parquet_components) {
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expect_true(grepl("\\.parquet$", metadata(obj)[[component]]))
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}
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# Dimensions
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input <- readXeniumSXE(
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dirName = spe,
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returnType = "SPE"
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)
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dim_rds <- dim(obj)
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dim_input <- dim(input)
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expect_equal(dim_rds, dim_input)
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cat("> Checking parameter functionality\n")
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out_rds_ext <- "output_ext.rds"
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cat("> Running ", meta[["name"]], "\n", sep = "")
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out_ext <- processx::run(
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meta[["executable"]],
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c(
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"--input", spe,
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"--add_experiment_xenium", FALSE,
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"--add_parquet_paths", FALSE,
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"--alternative_experiment_features", c("NegControlProbe"),
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"--output", out_rds_ext
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)
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)
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cat("> Checking whether output file exists\n")
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expect_equal(out_ext$status, 0)
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expect_true(file.exists(out_rds_ext))
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cat("> Reading output file\n")
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obj_ext <- readRDS(file = out_rds_ext)
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cat("> Checking whether Seurat object is in the right format\n")
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# Object type
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expect_is(obj_ext, "SpatialExperiment")
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# Assay structure
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expect_equal(names(slot(obj_ext, "assays")), "counts")
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# Spatial coordinates
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expect_equal(spatialCoordsNames(obj_ext), c("x_centroid", "y_centroid"))
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# Alternative experiments
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expect_equal(altExpNames(obj_ext), c("NegControlProbe"))
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# Metadata components
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expect_true(length(metadata(obj_ext)) == 0)
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dim_rds_ext <- dim(obj_ext)
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expect_true(identical(dim_rds_ext[2], dim_input[2]))
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expect_false(identical(dim_rds_ext[1], dim_input[1]))
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