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SCENIC_CART/export_loom.R

+library(Seurat)
+library(SCENIC)
+library(SCopeLoomR)
+library(dplyr)
+
+args <- commandArgs(trailingOnly = TRUE)
+
+# Input Seurat RDS file
+in_rds <- args[1]
+# Output
+out_loom <- args[2]
+
+in_obj <- readRDS(in_rds)
+assay_name <- "RNA"
+if (!assay_name %in% names(in_obj@assays)) {
+  assay_name <- names(in_obj@assays)[1]
+  print("'RNA' assay not found!")
+  print(paste0("Using ", assay_name, " as assay."))
+}
+
+umap_vars <- grep("umap", names(in_obj@reductions), value = T)
+umap_name <- grep("harmony", umap_vars, value = T)
+if (length(umap_name == 0)) {
+  umap_name <- umap_vars[1]
+}
+umap <- as.data.frame(in_obj@reductions[[umap_name]]@cell.embeddings)
+colnames(umap) <- c("X", "Y")
+cm <- in_obj@assays[[assay_name]]
+cm <- as.matrix(cm$counts)
+loom <- build_loom(file.name = out_loom, dgem = cm, default.embedding = umap, default.embedding.name = "umap")
+loom <- add_cell_annotation(loom = loom, cellAnnotation = in_obj@meta.data)
+close_loom(loom = loom)