H5mu to seurat

CHANGELOG.md

@@ -1,3 +1,9 @@
+# openpipeline_spatial x.x.x
+
+## NEW FUNCTIONALITY
+
+* `convert/from_h5mu_to_seurat`: Added converter component for H5MU data to Seurat objects with spatial FOV (PR #23).
+
 # openpipeline_spatial 0.1.1
 
 ## MINOR CHANGES

src/convert/from_cosmx_to_spatialexperiment/test.R

@@ -75,8 +75,9 @@ spe <- paste0(meta[["resources_dir"]], "/Lung5_Rep2_tiny")
 out_rds <- "output.rds"
 
 create_folder_archive <- function(
-    folder_path,
-    archive = "Lung5_Rep2_tiny.zip") {
+  folder_path,
+  archive = "Lung5_Rep2_tiny.zip"
+) {
   old_wd <- getwd()
   on.exit(setwd(old_wd))
   setwd(meta$resources_dir)

src/convert/from_h5mu_to_seurat/config.vsh.yaml

@@ -0,0 +1,88 @@
+name: "from_h5mu_to_seurat"
+namespace: "convert"
+scope: "public"
+description: |
+  Converts an h5ad file or a single modality of an h5mu file into a Seurat file with a Field of View (FOV) field, 
+  storing coordinates of spatially-resolved single cells based on centroid coordinates.
+authors:
+  - __merge__: /src/authors/dorien_roosen.yaml
+    roles: [ author, maintainer ]
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: "--input"
+      alternatives: ["-i"]
+      type: file
+      description: Input h5ad or h5mu file
+      direction: input
+      required: true
+      example: input.h5ad
+    - name: "--modality"
+      type: string
+      default: "rna"
+      required: true
+      description: Modality to be converted if the input file is an h5mu file.
+    - name: "--obsm_centroid_coordinates"
+      type: string
+      description: |
+        Key name of the .obsm slot in the input file that contains the spatial (centroid) coordinates.
+        If not provided, no Field of View (FOV) will be created in the Seurat object.
+  - name: Centroid arguments
+    arguments:
+    - name: "--centroid_nsides"
+      type: integer
+      required: false
+      description: |
+        Number of sides of the polygon to be created around each centroid coordinate to represent the cell shape.
+        If not provided, circles will be created.
+    - name: "--centroid_radius"
+      type: double
+      required: false
+      description: |
+        Radius of the shape around each centroid coordinate to represent the cell shape.
+        If not provided, a default radius will be calculated based on the provided centroid coordinates.
+    - name: "--centroid_theta"
+      type: double
+      required: false
+      description: |
+        Angle to adjust the shapes around each centroid when plotting.
+        If not provided, no adjustment will be made (theta = 0)
+  - name: Outputs
+    arguments:
+    - name: "--output"
+      alternatives: ["-o"]
+      type: file
+      description: Output Seurat file
+      direction: output
+      required: true
+      example: output.rds
+    - name: "--assay"
+      type: string
+      default: "RNA"
+      description: Name of the assay to be created.
+resources:
+  - type: r_script
+    path: script.R
+test_resources:
+  - type: r_script
+    path: test.R
+  - path: /resources_test/aviti/aviti_teton_tiny.h5mu
+  - path: /resources_test/cosmx/Lung5_Rep2_tiny.h5mu
+  - path: /resources_test/xenium/xenium_tiny.h5mu
+engines:
+  - type: docker
+    image: rocker/r2u:22.04
+    setup:
+      - type: apt
+        packages: [ libhdf5-dev, libgeos-dev, hdf5-tools ]
+      - type: r
+        cran: [ anndata, hdf5r, Seurat, SeuratObject ]
+        github: scverse/anndataR@36f3caad9a7f360165c1510bbe0c62657580415a
+    test_setup:
+      - type: r
+        cran: [ testthat ]
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [lowmem, singlecpu]

src/convert/from_h5mu_to_seurat/script.R

@@ -0,0 +1,93 @@
+library(anndataR)
+library(hdf5r)
+library(Seurat)
+
+### VIASH START
+par <- list(
+  input = "resources_test/xenium/xenium_tiny_processed.h5mu",
+  output = "test.rds",
+  obsm_centroid_coordinates = "spatial",
+  assay = "RNA",
+  centroid_nsides = 8,
+  centroid_radius = 3,
+  centroid_theta = 0.1,
+  modality = "rna"
+)
+### VIASH END
+
+
+h5mu_to_h5ad <- function(h5mu_path, modality_name) {
+  tmp_path <- tempfile(fileext = ".h5ad")
+  mod_location <- paste("mod", modality_name, sep = "/")
+  h5src <- hdf5r::H5File$new(h5mu_path, "r")
+  h5dest <- hdf5r::H5File$new(tmp_path, "w")
+  # Copy over the child objects and the child attributes from root
+  children <- hdf5r::list.objects(h5src,
+    path = mod_location,
+    full.names = FALSE, recursive = FALSE
+  )
+  for (child in children) {
+    h5dest$obj_copy_from(
+      h5src, paste(mod_location, child, sep = "/"),
+      paste0("/", child)
+    )
+  }
+  # Also copy the root attributes
+  root_attrs <- hdf5r::h5attr_names(x = h5src)
+  for (attr in root_attrs) {
+    h5a <- h5src$attr_open(attr_name = attr)
+    robj <- h5a$read()
+    h5dest$create_attr_by_name(
+      attr_name = attr,
+      obj_name = ".",
+      robj = robj,
+      space = h5a$get_space(),
+      dtype = h5a$get_type()
+    )
+  }
+  h5src$close()
+  h5dest$close()
+
+  tmp_path
+}
+
+# Read in H5AD
+h5ad_path <- h5mu_to_h5ad(par$input, par$modality)
+
+# Convert to Seurat
+seurat_obj <- read_h5ad(
+  h5ad_path,
+  mode = "r",
+  as = "Seurat",
+  assay_name = par$assay
+)
+
+# Create Centroids object
+if (!is.null(par$obsm_centroid_coordinates)) {
+  reductions <- seurat_obj@reductions[[par$obsm_centroid_coordinates]]
+  spatial_coords <- as.data.frame(reductions@cell.embeddings)
+  colnames(spatial_coords) <- c("x_coord", "y_coord")
+
+  if (is.null(par$centroid_nsides)) {
+    par$centroid_nsides <- Inf
+  }
+
+  if (is.null(par$centroid_theta)) {
+    par$centroid_theta <- 0L
+  }
+
+  centroids <- CreateCentroids(
+    coords = spatial_coords,
+    nsides = par$centroid_nsides,
+    radius = par$centroid_radius,
+    theta = par$centroid_theta
+  )
+
+  # Create FOV object
+  fov <- CreateFOV(coords = centroids, assay = par$assay)
+  seurat_obj[["fov"]] <- fov
+  seurat_obj@reductions[[par$obsm_centroid_coordinates]] <- NULL
+}
+
+
+saveRDS(seurat_obj, file = par$output)