add poi script

Author: littlecabiria

src/methods/scdesign3_poisson/script.R

@@ -0,0 +1,74 @@
+suppressMessages(library(SingleCellExperiment, quietly = TRUE))
+suppressMessages(library(scDesign3, quietly = TRUE))
+
+## VIASH START
+par <- list(
+  input = "resources_test/spatialsimbench_mobnew/MOBNEW.rds",
+  base = "domain",
+  output = "simulated_dataset.h5ad",
+  family = "poi",
+  usebam = FALSE
+)
+meta <- list(
+  name = "scdesign3"
+)
+## VIASH END
+reticulate::py_config()
+cat("Read input files\n")
+input <- anndata::read_h5ad(par$input)
+
+sce <- SingleCellExperiment(
+  list(counts = Matrix::t(input$layers[["counts"]])),
+  colData = input$obs
+)
+
+cat("scDesign3 Simulation Start\n")
+
+if (par$base == "tissue") {
+  sce@colData$cell_type <- "cell_type"
+} else if (par$base == "domain") {
+  sce@colData$cell_type <- as.character(sce@colData$spatial_cluster)
+} else {
+  stop("wrong base parameter")
+}
+
+sce_simu <- scdesign3(
+  sce = sce,
+  assay_use = "counts",
+  celltype = "cell_type",
+  pseudotime = NULL,
+  spatial = c("row", "col"), # spatial location
+  other_covariates = NULL,
+  mu_formula = "s(row, col, bs = 'gp', k = 100)",
+  sigma_formula = "1",
+  family_use = par$family, # could be change another distribution
+  n_cores = 1,
+  usebam = par$usebam,
+  corr_formula = "1",
+  copula = "gaussian",
+  DT = TRUE,
+  pseudo_obs = FALSE,
+  return_model = FALSE,
+  nonzerovar = FALSE,
+  parallelization = "mcmapply"
+)
+
+cat("Generating output file\n")
+new_obs <- sce_simu$new_covariate[c("row", "col")]
+
+output <- anndata::AnnData(
+  layers = list(
+    counts = Matrix::t(sce_simu$new_count)
+  ),
+  obs = new_obs,
+  var = input$var,
+  uns = c(
+    input$uns,
+    list(
+      method_id = meta$name
+    )
+  )
+)
+
+cat("Write output files\n")
+output$write_h5ad(par$output, compression = "gzip")