From 0299e56fc8df98058c6e1add3b2a84e20042e82f Mon Sep 17 00:00:00 2001
From: Dillon Hammill <dillon.hammill@ozette.com>
Date: Tue, 5 Nov 2024 12:42:14 +1100
Subject: [PATCH] ODC-180 merge all samples when groupBy = NA and
 CollapseDataFroGating = TRUE.

---
 R/gating-methods.R       | 3 +++
 R/preprocessing-method.R | 8 ++++----
 2 files changed, 7 insertions(+), 4 deletions(-)

diff --git a/R/gating-methods.R b/R/gating-methods.R
index a6f3a4d..ad2719b 100644
--- a/R/gating-methods.R
+++ b/R/gating-methods.R
@@ -290,6 +290,9 @@ roxygen_parameter <- function() {
         split_by <- apply(pData(parent_data)[, split_by, drop = FALSE], 1, paste, collapse = ":")
         split_by <- as.character(split_by)
       }
+    # all samples same group - labeled "all"
+    } else if(groupBy == "" && isCollapse) {
+      split_by <- rep("all", length(parent_data))
     } else {
       split_by <- sampleNames(parent_data)
     }
diff --git a/R/preprocessing-method.R b/R/preprocessing-method.R
index e5a72c9..593c87d 100644
--- a/R/preprocessing-method.R
+++ b/R/preprocessing-method.R
@@ -83,10 +83,10 @@ update_list <- function (x, val)
         split_by <- as.character(split_by)
       }
       fslist <- split(parent_data, split_by)
-    }else 
-    {
-      fslist <- list(parent_data)  
-    } 
+    }else {
+      # all samples same group named "all" - matches .gating_gtMethod()
+      fslist <- list("all" = parent_data)  
+    }
     
     # construct method call
     thisCall <- substitute(f1())