fix bugs

.gitignore

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

R/SCP-analysis.R

@@ -482,7 +482,7 @@ FindCorrelatedFeatures <- function(srt, feature, method = "ejaccard", assay = NU
   assay <- assay %||% DefaultAssay(srt)
   x <- as_matrix(t(FetchData(srt, feature)))
   y <- GetAssayData(srt, assay = assay, slot = slot)
-  out <- proxyC::simil(x = x, y = y, method = "ejaccard", use_nan = TRUE)
+  out <- proxyC::simil(x = x, y = y, method = method, use_nan = TRUE)
   out[is.na(out)] <- 0
   out <- sort(out[1, ], decreasing = T)
   return(out)
@@ -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"))

R/SCP-cell_annotation.R

@@ -436,7 +436,7 @@ RunKNNPredict <- function(srt_query, srt_ref = NULL, bulk_ref = NULL,
       match_prob <- do.call(rbind, lapply(match_freq, function(x) {
         x[level[!level %in% names(x)]] <- 0
         x <- x / sum(x)
-        return(x)
+        return(x[level])
       }))
       match_prob <- as_matrix(match_prob)
       rownames(match_prob) <- names(match_freq)