CI
13b9f1b077
Build pipeline: openpipelines-bio.openpipeline-spatial.update-mudata-pssvw
Source commit: 2f7991091d
Source message: linting
114 lines
3.2 KiB
R
114 lines
3.2 KiB
R
library(SpatialExperiment)
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library(SingleCellExperiment)
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library(hdf5r)
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library(Matrix)
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library(hdf5r)
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## VIASH START
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par <- list(
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input = "resources_test/xenium/xenium_tiny.h5mu",
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output = "xenium_test.rds",
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modality = "rna",
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obsm_spatial_coordinates = "spatial"
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)
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## VIASH END
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h5mu_to_h5ad <- function(h5mu_path, modality_name) {
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tmp_path <- tempfile(fileext = ".h5ad")
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mod_location <- paste("mod", modality_name, sep = "/")
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h5src <- hdf5r::H5File$new(h5mu_path, "r")
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h5dest <- hdf5r::H5File$new(tmp_path, "w")
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# Copy over the child objects and the child attributes from root
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# Root cannot be copied directly because it always exists and
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# copying does not allow overwriting.
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children <- hdf5r::list.objects(h5src,
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path = mod_location,
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full.names = FALSE, recursive = FALSE
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)
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for (child in children) {
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h5dest$obj_copy_from(
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h5src, paste(mod_location, child, sep = "/"),
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paste0("/", child)
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)
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}
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# Also copy the root attributes
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root_attrs <- hdf5r::h5attr_names(x = h5src)
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for (attr in root_attrs) {
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h5a <- h5src$attr_open(attr_name = attr)
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robj <- h5a$read()
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h5dest$create_attr_by_name(
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attr_name = attr,
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obj_name = ".",
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robj = robj,
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space = h5a$get_space(),
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dtype = h5a$get_type()
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)
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}
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h5src$close()
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h5dest$close()
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tmp_path
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}
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read_spatial_coordinates <- function(sce, spatial_coordinates_name) {
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# Check if the specified spatial coordinates exist in reducedDims
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reduced_dims <- SingleCellExperiment::reducedDims(sce)
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if (par$obsm_spatial_coordinates %in% names(reduced_dims)) {
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spatial_coords <- reduced_dims[[par$obsm_spatial_coordinates]]
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if (ncol(spatial_coords) != 2) {
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stop(
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"Spatial coordinates must have 2 columns, but found ",
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ncol(spatial_coords), " columns"
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)
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}
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# Set proper column names for spatial coordinates
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colnames(spatial_coords) <- c("x", "y")
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} else {
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warning(
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"Spatial coordinates '", par$obsm_spatial_coordinates,
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"' not found in reducedDims. Available dimensions: ",
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paste(names(reduced_dims), collapse = ", ")
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)
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spatial_coords <- NULL
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}
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spatial_coords
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}
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main <- function() {
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# Convert to AnnData
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cat("Converting H5MU file to H5AD...\n")
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h5file <- h5mu_to_h5ad(par$input, par$modality)
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# Convert to SpatialExperiment
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cat("Converting to SingleCellExperiment...\n")
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sce <- anndataR::read_h5ad(h5file, as = "SingleCellExperiment")
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# Extract spatial coordinates if specified
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if (
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!is.null(par$obsm_spatial_coordinates) &&
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length(par$obsm_spatial_coordinates) > 0
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) {
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cat("Reading in spatial coordinates...\n")
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spatial_coords <- read_spatial_coordinates(
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sce, par$obsm_spatial_coordinates
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)
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SingleCellExperiment::reducedDims(sce)[[
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par$obsm_spatial_coordinates
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]] <- NULL
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} else {
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spatial_coords <- NULL
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}
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# Converting SingleCellExperiment to SpatialExperiment
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cat("Converting to SpatialExperiment...\n")
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spe <- as(sce, "SpatialExperiment")
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SpatialExperiment::spatialCoords(spe) <- spatial_coords
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# Saving SpatialExperiment object
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cat("Saving SpatialExperiment object to:", par$output, "\n")
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saveRDS(spe, file = par$output, compress = FALSE)
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}
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main()
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