Merge pull request #14 from openproblems-bio/spanorm

spanorm is runable

Author: LouisK92

src/methods_normalization/spanorm/config.vsh.yaml

@@ -0,0 +1,39 @@
+__merge__: /src/api/comp_method_normalization.yaml
+
+name: spanorm
+label: "SpaNorm normalization"
+summary: "Spatially-aware normalisation for spatial transcriptomics data"
+description: "Spatially-aware normalisation for spatial transcriptomics data"
+links:
+  documentation: "https://github.com/openproblems-bio/task_ist_preprocessing"
+  repository: "https://github.com/bhuvad/SpaNorm/tree/master"
+references:
+  doi: "10.1101/2024.05.31.596908"
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1
+    setup:
+      - type: r
+        bioc: [SpaNorm, zellkonverter]
+      #- type: r
+      #  bioc: [SummarizedExperiment,SingleCellExperiment,SpatialExperiment]
+      #  bioc_force_install: true
+      - type: docker
+        run: |
+          Rscript -e "BiocManager::install('SingleCellExperiment', type = 'source', force = TRUE, ask = FALSE)"
+      # This can probably be left out again in the future. It currently fixes a bug described in these issues:
+      # https://github.com/drighelli/SpatialExperiment/issues/171
+      # https://github.com/satijalab/seurat/issues/9889
+      # The reinstall of SingleCellExperiment triggers the correct re-install of SpatialExperiment.
+  - type: native
+
+runners:
+  - type: executable
+  - type: nextflow
+    directives:
+      label: [ midtime, lowcpu, lowmem ]

src/methods_normalization/spanorm/script.R

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+library(SpaNorm)
+library(SingleCellExperiment)
+library(SpatialExperiment)
+library(zellkonverter)
+
+## VIASH START
+par <- list(
+  "input_spatial_aggregated_counts" = 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_aggregated_counts.h5ad',
+  "output" = 'tmp/spatial_spanormed_counts.h5ad'
+)
+## VIASH END
+
+# Read the input h5ad file and convert to SingleCellExperiment
+sce <- readH5AD(par$input_spatial_aggregated_counts)
+# Convert to SpatialExperiment for SpaNorm
+sce <- as(sce, "SpatialExperiment")
+
+# Extract spatial coordinates
+centroid_x <- colData(sce)$centroid_x
+centroid_y <- colData(sce)$centroid_y
+
+# Create spatial coordinates matrix for SpaNorm
+spatial_coords <- matrix(c(centroid_x, centroid_y), ncol = 2)
+
+# Set spatial coordinates in the SpatialExperiment object
+spatialCoords(sce) <- spatial_coords
+
+# Apply SpaNorm normalization to the spatial data
+result <- SpaNorm(sce)
+
+# Get the normalized matrix from SpaNorm result (log-transformed normalized counts)
+normalized_matrix <- assay(result, "logcounts")
+
+# Create final SCE with all original layers preserved
+final_sce <- SingleCellExperiment(
+  assays = assays(sce),  # Preserve all original assays
+  rowData = rowData(sce),
+  colData = colData(sce)
+)
+
+# Add the normalized matrix as a new layer called 'normalized'
+assay(final_sce, "normalized") <- normalized_matrix
+
+# Write the final object to h5ad format
+zellkonverter::writeH5AD(final_sce, par$output)