spanorm is runable

.Rhistory

@@ -0,0 +1,78 @@
+library(SpaNorm)
+devtools::install_github("bhuvad/SpaNorm")
+install.packages(""\\wsl.localhost\Ubuntu\home\astat17\task_ist_preprocessing\SpaNorm"", repos = NULL, type = "source")
+install.packages(""wsl.localhost\Ubuntu\home\astat17\task_ist_preprocessing\SpaNorm"", repos = NULL, type = "source")
+install.packages("wsl.localhost\Ubuntu\home\astat17\task_ist_preprocessing\SpaNorm", repos = NULL, type = "source")
+install.packages("wsl.localhost/Ubuntu/home/astat17/task_ist_preprocessing/SpaNorm", repos = NULL, type = "source")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("SpaNorm")
+library(SpaNorm)
+ installed.packages()[, "Package"]
+install.packages("textshaping", type = "source", configure.vars = "INCLUDE_DIR=/path/to/include LIB_DIR=/path/to/lib")
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("SpaNorm")
+library(SpaNorm)
+install.packages("textshaping")
+install.packages("SpaNorm")
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("SpaNorm")
+if (!require("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install(version = "3.19")
+BiocManager::version()
+BiocManager::install(version = "3.19")
+BiocManager::version()
+BiocManager::install(c(
+    "SummarizedExperiment",
+    "GenomicRanges",
+    "DelayedArray",
+    "SingleCellExperiment",
+    "scuttle",
+    "SpatialExperiment",
+    "scran",
+    "beachmat",
+    "BiocSingular",
+    "SparseArray"
+))
+if (!requireNamespace("devtools", quietly = TRUE)) {
+  install.packages("devtools")
+}
+library(devtools)
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install(version = "3.18")
+BiocManager::version()
+BiocManager::install("SpaNorm", dependencies = TRUE)
+BiocManager::install(c( "DelayedArray",  "ScaledMatrix",  "beachmat", "GenomicRanges", "SummarizedExperiment",  "SingleCellExperiment",  "BiocSingular",  "scuttle",  "scran","SpatialExperiment" ))
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install(c( "DelayedArray",  "ScaledMatrix",  "beachmat", "GenomicRanges", "SummarizedExperiment",  "SingleCellExperiment",  "BiocSingular",  "scuttle",  "scran","SpatialExperiment" ))
+install.packages("wsl.localhost/Ubuntu/home/astat17/task_ist_preprocessing/SpaNorm", repos = NULL, type = "source")
+install.packages("\\\\wsl$\\Ubuntu\\home\\astat17\\task_ist_preprocessing\\SpaNorm", repos = NULL, type = "source")
+install.packages("/home/astat17/task_ist_preprocessing/SpaNorm", repos = NULL, type = "source")
+install.packages(c('edgeR', 'ggplot2', 'Matrix', 'matrixStats', 'rlang', 
+                   'scran', 'SeuratObject', 'SingleCellExperiment', 
+                   'SpatialExperiment', 'SummarizedExperiment', 'S4Vectors'))
+library(scran)
+.libPaths(c("C:/Program Files/R/R-4.4.1/library", .libPaths()))
+library(SpaNorm)
+library(spanorm)
+.libPaths()
+install.packages("matrixStats")
+install.packages("S4Vectors")
+install.packages("S4Vectors")
+if (.Platform$OS.type == "windows") {
+    utils::winMenuAddItem("MyMenu", "MyItem")
+}
+if (!requireNamespace("BiocManager", quietly = TRUE))
+    install.packages("BiocManager")
+BiocManager::install("SpaNorm")
+library(SpaNorm)
+assign(".Platform", list(OS.type = "windows"), envir = baseenv())
+if (.Platform$OS.type == "windows") {
+    utils::winMenuAddItem("MyMenu", "MyItem")
+}
+library(SpaNorm)

src/methods_normalization/spanorm/config.vsh.yaml

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+__merge__: /src/api/comp_method_normalization.yaml
+
+name: spanorm
+label: "Spatially-aware normalisation for spatial transcriptomics data"
+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: "https://doi.org/10.1101/2024.05.31.596908"
+
+resources:
+  - type: r_script
+    path: script.R
+
+engines:
+  - type: docker
+    image: openproblems/base_r:1.0.0
+    setup:
+      - type: r
+        bioc: SpaNorm, zellkonverter
+  - 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)
+
+par <- list(
+  "input" = 'resources_test/task_ist_preprocessing/mouse_brain_combined/spatial_aggregated_counts.h5ad',
+  "output" = 'tmp/spatial_spanormed_counts.h5ad'
+)
+
+sce <- readH5AD(par$input)
+sce <- as(sce, "SpatialExperiment")
+
+centroid_x <- colData(sce)$centroid_x
+centroid_y <- colData(sce)$centroid_y
+
+spatial_coords <- matrix(c(centroid_x, centroid_y), ncol = 2)
+
+spatialCoords(sce) <- spatial_coords
+
+keep = filterGenes(sce, 0.05)
+sce <- sce[keep, ]
+result <- SpaNorm(sce)
+
+main_assay <- assay(result, "X")
+row_data <- rowData(result)
+col_data <- colData(result)
+
+final_sce <- SingleCellExperiment(
+  assays = list(X = main_assay),
+  rowData = row_data,
+  colData = col_data
+)
+
+zellkonverter::writeH5AD(final_sce, par$output)