@@ -272,6 +272,8 @@ setMethod("check_parent_child_coherence", c("obj" = "SingleCellExperiment"),

 })

 #' Filter cells from ambiguous chars and non applicable cells

+#' Ambiguous characters includes: "/", ",", "-", "+", ".", "and", 

+#' "or", "(", ")", "ambiguous"

 #' 

 #' @param obj object

 #' @param tag_slot slot in cell meta data indicating cell type

@@ -290,8 +292,8 @@ setGeneric("filter_cells", function(obj, tag_slot)

 setMethod("filter_cells", c("obj" = "Seurat"), function(obj, tag_slot) {

   # define characters usually included in ambiguous cell types

   # this is to avoid considering ambiguous cell types as negative cell_type

-  ambiguous.chars <- c("/", ",", " -", " [+]", "[.]", "and", 

-                       "or", "[(]" ,"[)]", "ambiguous")

+  ambiguous.chars <- c("/", ",", " -", " [+]", "[.]", " and ", 

+                       " or ", "_or_", "-or-", "[(]" ,"[)]", "ambiguous")

   # only eliminate cell labels containing cell_type and ambiguous.chars

   if (tag_slot == "active.ident") {

@@ -311,7 +313,10 @@ setMethod("filter_cells", c("obj" = "Seurat"), function(obj, tag_slot) {

   n.applicable.cells <- 

     rownames(cell.tags[grepl("not applicable", cell.tags[, 1]) 

                        | is.na(cell.tags[, 1]),, drop = FALSE])

-  

+  if (any(ambiguous))

+    warning('Cell types containing "/", ",", "-", "+", ".", "and", "or", "(", 

+            ")", and "ambiguous" are considered as ambiguous. They are removed

+            from training and testing.', call. = FALSE, immediate. = TRUE)

   keeping.cells <- 

     colnames(obj)[!((colnames(obj) %in% ambiguous.cells) 

                     | colnames(obj) %in% n.applicable.cells)]

@@ -346,6 +351,10 @@ setMethod("filter_cells", c("obj" = "SingleCellExperiment"),

   ambiguous <- grepl(paste(ambiguous.chars, collapse="|"), cell.tags)

   n.applicable <- (grepl("not applicable", cell.tags) | is.na(cell.tags))

+  if (any(ambiguous))

+    warning('Cell types containing "/", ",", "-", "+", ".", "and", "or", "(", 

+            ")", and "ambiguous" are considered as ambiguous. They are removed

+            from training and testing.', call. = FALSE, immediate. = TRUE)

   obj <- obj[, !(ambiguous | n.applicable)]

   return(obj)