fix bugs

.gitignore

@@ -11,4 +11,5 @@ tmaps
 src/*.so
 src/*.o
 test.R
-test.cpp
+test.cpp
+test

R/SCP-analysis.R

@@ -3996,6 +3996,8 @@ RunEnrichment <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_t
   results <- results[!sapply(results, is.null)]
   results <- results[intersect(c(nm, paste0(nm, "_sim")), names(results))]
   enrichment <- do.call(rbind, lapply(results, function(x) x@result))
+  enrichment[["Groups"]] <- factor(enrichment[["Groups"]], levels = levels(geneID_groups))
+  enrichment[["Database"]] <- factor(enrichment[["Database"]], levels = unique(enrichment[["Database"]]))
   rownames(enrichment) <- NULL
 
   time_end <- Sys.time()
@@ -4293,6 +4295,8 @@ RunGSEA <- function(srt = NULL, group_by = NULL, test.use = "wilcox", DE_thresho
   results <- results[!sapply(results, is.null)]
   results <- results[intersect(c(nm, paste0(nm, "_sim")), names(results))]
   enrichment <- do.call(rbind, lapply(results, function(x) x@result))
+  enrichment[["Groups"]] <- factor(enrichment[["Groups"]], levels = levels(geneID_groups))
+  enrichment[["Database"]] <- factor(enrichment[["Database"]], levels = unique(enrichment[["Database"]]))
   rownames(enrichment) <- NULL
 
   time_end <- Sys.time()

R/SCP-app.R

@@ -595,7 +595,7 @@ RunSCExplorer <- function(base_dir = "SCExplorer",
                           initial_raster = NULL,
                           session_workers = 2,
                           plotting_workers = 8,
-                          create_script = FALSE,
+                          create_script = TRUE,
                           style_script = require("styler", quietly = TRUE),
                           overwrite = FALSE) {
   check_R(c("rhdf5", "HDF5Array", "[email protected]", "ggplot2", "ragg", "htmlwidgets", "plotly", "bslib", "future", "promises", "BiocParallel"))