Merge pull request #265 from longmanz/fix_subset_assay5_bug

make tryCatch in subset.Seurat() handles more error messages from subset.Assay5()

Author: anashen

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: SeuratObject
 Title: Data Structures for Single Cell Data
-Version: 5.3.0.9001
+Version: 5.3.0.9002
 Authors@R: c(
   person(given = 'Paul', family = 'Hoffman', email = 'hoff0792@alumni.umn.edu', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),
   person(given = 'Rahul', family = 'Satija', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),

R/seurat.R

@@ -3782,7 +3782,9 @@ subset.Seurat <- function(
             classes = 'validationWarning'
           ),
           error = function(e) {
-            if (e$message == "Cannot find features provided") {
+            if (e$message %in% c("Cannot find features provided", 
+                                 "None of the features provided found in this assay")
+            ) {
               return(NULL)
             } else {
               stop(e)
@@ -3796,9 +3798,11 @@ subset.Seurat <- function(
     f = Negate(f = is.null),
     x = slot(object = x, name = 'assays')
   )
-  if (length(x = .FilterObjects(object = x, classes.keep = c('Assay', 'StdAssay'))) == 0 || is.null(x = x[[DefaultAssay(object = x)]])) {
+  if (length(x = .FilterObjects(object = x, classes.keep = c('Assay', 'StdAssay'))) == 0 ||
+      !DefaultAssay(object = x) %in% names(slot(object = x, name = 'assays'))) {
     abort(message = "Under current subsetting parameters, the default assay will be removed. Please adjust subsetting parameters or change default assay")
   }
+  
   # Filter DimReduc objects
   for (dimreduc in .FilterObjects(object = x, classes.keep = 'DimReduc')) {
     suppressWarnings(