@sjcrh/proteinpaint-server 2.65.0 → 2.66.0

package/utils/getGeneFromMatrix.R

@@ -0,0 +1,40 @@
+library(jsonlite)
+library(Matrix)
+
+# This script assumes the .Rds file is a gene
+# by sample matrix. Use this script to extract
+# the values per sample for a particular gene.
+
+args <- commandArgs(trailingOnly = TRUE)
+if (length(args) == 0) {
+  stop("No arguments provided.")
+}
+
+# str
+file_path <- args[1]
+# str
+gene_name <- args[2]
+
+data <- tryCatch({
+  readRDS(file_path)
+}, error = function(e) {
+  # Show error if file is not found or cannot be read 
+  # (i.e. not an RDS file)
+  stop(paste("Error reading RDS file:", e$message))
+})
+
+# Show error if gene not found
+if (!(gene_name %in% rownames(data))) {
+  stop(paste("Gene", gene_name, "not found in the matrix."))
+}
+
+# Extract the gene data and filter out zero values
+gene_data <- data[gene_name, ]
+non_zero_indices <- gene_data != 0
+filtered_samples <- colnames(data)[non_zero_indices]
+filtered_values <- as.numeric(gene_data[non_zero_indices])
+
+# Create a JSON object with the samples as the keys and the
+# values as the values, e.g. {"sample1": 1, "sample2": 2, ...n }
+result <- setNames(as.list(filtered_values), filtered_samples)
+toJSON(result, pretty = TRUE, auto_unbox = TRUE)