WT: Updated documentation and added support for setting resolution for RNA-seq analyses

Author: williamthistle

R/process_batches.R

@@ -431,13 +431,14 @@ IntegrateByBatch_ATAC <- function(proj, output_dir = getwd(), exit_with_code = F
 #'
 #' @param sc_obj Seurat object containing cells for all samples
 #' @param output_dir Path to directory where output will be saved. Defaults to working directory ([getwd()]).
+#' @param resolution Resolution used for clustering
 #' @param exit_with_code Boolean flag to indicate whether we will terminate R session with exit code (via [quit()]) if error occurs. If set to FALSE, we just use [stop()].
 #' @param log_flag If set to TRUE, record certain output (e.g., parameters) to a previously set up log file. Most likely only used in the context of [run_SPEEDI()].
 #' @return A Seurat object with SCT markers and visualizations
 #' @examples
 #' \dontrun{sc_obj <- VisualizeIntegration(sc_obj)}
 #' @export
-VisualizeIntegration <- function(sc_obj, output_dir = getwd(), exit_with_code = FALSE, log_flag = FALSE) {
+VisualizeIntegration <- function(sc_obj, output_dir = getwd(), resolution = 2, exit_with_code = FALSE, log_flag = FALSE) {
   exit_code <- -1
   sc_obj <- tryCatch(
     {
@@ -458,7 +459,7 @@ VisualizeIntegration <- function(sc_obj, output_dir = getwd(), exit_with_code =
       } else {
         print_SPEEDI("Neighbors exist. Skipping constructing neighborhood graph...", log_flag)
       }
-      sc_obj <- find_clusters_SPEEDI(sc_obj = sc_obj, resolution = 2, method = "Leiden", log_flag = log_flag)
+      sc_obj <- find_clusters_SPEEDI(sc_obj = sc_obj, resolution = resolution, method = "Leiden", log_flag = log_flag)
       sample_count <- length(unique(sc_obj$sample))
       cell_count <- length(sc_obj$cell_name)
       # Plot by cluster

R/wrapper.R

@@ -87,7 +87,7 @@ run_SPEEDI <- function(reference_tissue, data_type = "RNA", species = "human", i
                            log_flag = SPEEDI_variables$log_flag)
     sc_obj <- IntegrateByBatch_RNA(sc_obj = sc_obj, exit_with_code = SPEEDI_variables$exit_with_code,
                                    log_flag = SPEEDI_variables$log_flag)
-    sc_obj <- VisualizeIntegration(sc_obj = sc_obj, output_dir = SPEEDI_variables$RNA_output_dir,
+    sc_obj <- VisualizeIntegration(sc_obj = sc_obj, output_dir = SPEEDI_variables$RNA_output_dir, resolution = 2,
                                    exit_with_code = SPEEDI_variables$exit_with_code, log_flag = SPEEDI_variables$log_flag)
   }
   if(data_type != "RNA") {