Ajout script pour récupération données

retrieve-data.R

@@ -6,3 +6,32 @@ if ("MicroBioMap" %in% rownames(installed.packages()) == FALSE) {
     BiocManager::install("blekhmanlab/MicroBioMap")
 }
 library(MicroBioMap)
+library(countrycode)
+library(igraph)
+library(here)
+library(readr)
+setClassUnion("ExpData", c("matrix", "SummarizedExperiment"))
+cpd <- getCompendium(version = "1.0.1")
+
+colData(cpd)$country <- countrycode(colData(cpd)$iso, "iso2c", "country.name")
+
+projects <- unique(colData(cpd)$project)
+
+save_folder <- here("data")
+if (!dir.exists(save_folder)) {
+    dir.create(save_folder)
+}
+
+for (project in projects) {
+    cat("Processing project:", project, "\n")
+    # Filter the compendium for the current project
+    project_data <- cpd[, colData(cpd)$project == project]
+    matrix_data <- counts(project_data)
+    # Create a graph from the matrix data
+    g <- graph_from_biadjacency_matrix(matrix_data)
+    edge_list <- as_edgelist(g) |> as.data.frame()
+    colnames(edge_list) <- c("source", "target")
+    write_csv(edge_list, file = here(save_folder, paste0(project, "_edge_list.csv.gz")))
+    supinfo_df <- as.data.frame(colData(project_data))
+    write_csv(supinfo_df, file = here(save_folder, paste0(project, "_supinfo.csv.gz")))
+}