changes data path to be able to run the app outside the cluster_comp_data folder

sc_workflow/sc_apps/clustering_explorer

@@ -24,7 +24,7 @@ load_pack(Seurat)
 
 # Determine data directory from execution context  ---------------------------------------------------------------------
 
-dataPath= args[1]
+dataPath= paste0(args[1], "cluster_comp_data")
 #dataPath = "."
 
 
@@ -32,10 +32,10 @@ dataPath= args[1]
 # LOAD data ------------------------------------------------------------------------------------------------------------
 
 # check presence of all required data
-all_files <- list.files(dataPath)
+all_files <- list.files(dataPath, pattern = ".txt")
 files_req <- c("cluster_info", "cluster_marker_genes", "scaled_counts", "tsne_info")
 
-if (any(!str_detect(files_req, paste0(files_req, collapse = "|")))) { stop("ATTENTION: please make sure cluster_info_*.txt, cluster_marker_genes_*.txt, scaled_counts.txt and tsne_info_*.txt exist in your working directory") }
+if (any(!str_detect(all_files, paste0(files_req, collapse = "|")))) { stop("ATTENTION: please make sure cluster_info_*.txt, cluster_marker_genes_*.txt, scaled_counts.txt and tsne_info_*.txt exist in your working directory") }
 
 
 # load all files
@@ -43,8 +43,8 @@ samples <- list.files(dataPath, pattern = "cluster_info_") %>% str_replace_all(.
 samples <- samples[order(nchar(samples), samples)]
 
 cluster_info <- do.call(rbind, lapply(samples, function(x){
-    tsne_info <- read_tsv(paste0("tsne_info_", x, ".txt"))
-    read_tsv(paste0("cluster_info_", x, ".txt")) %>%
+    tsne_info <- read_tsv(paste0(dataPath, "/tsne_info_", x, ".txt"))
+    read_tsv(paste0(dataPath, "/cluster_info_", x, ".txt")) %>%
         transmute(cell_id, cluster_num = cluster, cluster_name = paste0(x)) %>%
         left_join(tsne_info)
 })) %>%
@@ -56,7 +56,7 @@ cluster_info <- do.call(rbind, lapply(samples, function(x){
 
 
 marker_data <- lapply(setNames(samples, samples), function(x){
-    read_tsv(paste0("cluster_marker_genes_", x, ".txt")) %>%
+    read_tsv(paste0(dataPath, "/cluster_marker_genes_", x, ".txt")) %>%
         group_by(gene) %>%
         filter(1:n() == 1) %>%
         ungroup() %>%
@@ -76,7 +76,7 @@ marker_info <- do.call(rbind, lapply(names(marker_data), function(x) marker_data
     ungroup()
 
 
-count_data <- fread("scaled_counts.txt")
+count_data <- data.table::fread(paste0(dataPath, "/scaled_counts.txt"))
 gene_info <- select(count_data, ensembl_gene_id, external_gene_name, start_position, end_position, chromosome_name, description) %>%
     mutate(description = str_replace_all(description, "\\[Source:MGI Symbol;Acc:MGI:[:digit:]*]", ""))