From de553f0a8353fac2d1fa1de29837b71eae010121 Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Wed, 25 Sep 2024 14:26:57 -0500
Subject: [PATCH 1/2] add group.by to clonalOverlap and clonalQuant

Per issue #409
---
 R/clonalCompare.R | 5 +++++
 R/clonalOverlap.R | 5 +++++
 R/clonalQuant.R   | 2 +-
 3 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/R/clonalCompare.R b/R/clonalCompare.R
index a42432a9..e21f8863 100644
--- a/R/clonalCompare.R
+++ b/R/clonalCompare.R
@@ -74,6 +74,11 @@ clonalCompare <- function(input.data,
                               chain)
   cloneCall <- .theCall(input.data, cloneCall)
   
+  sco <- is_seurat_object(input.data) | is_se_object(input.data)
+  if(!is.null(group.by) & !sco) {
+    input.data <- .groupList(input.data, group.by)
+  }
+  
   Con.df <- NULL
   
   #Loop through the list to get a proportional summary
diff --git a/R/clonalOverlap.R b/R/clonalOverlap.R
index 742d8525..fd215862 100644
--- a/R/clonalOverlap.R
+++ b/R/clonalOverlap.R
@@ -89,6 +89,11 @@ clonalOverlap <- function(input.data,
     }
     
     cloneCall <- .theCall(input.data, cloneCall)
+    
+    sco <- is_seurat_object(input.data) | is_se_object(input.data)
+    if(!is.null(group.by) & !sco) {
+      input.data <- .groupList(input.data, group.by)
+    }
 
     num_samples <- length(input.data[])
     names_samples <- names(input.data)
diff --git a/R/clonalQuant.R b/R/clonalQuant.R
index 683dace6..01e7ed8a 100644
--- a/R/clonalQuant.R
+++ b/R/clonalQuant.R
@@ -49,8 +49,8 @@ clonalQuant <- function(input.data,
                               .theCall(input.data, cloneCall, check.df = FALSE), 
                               chain)
   cloneCall <- .theCall(input.data, cloneCall)
+  
   sco <- is_seurat_object(input.data) | is_se_object(input.data)
-
   if(!is.null(group.by) & !sco) {
     input.data <- .groupList(input.data, group.by)
   }

From a0d87a0f6db27395a6df5033113f0544292daeaa Mon Sep 17 00:00:00 2001
From: theHumanBorch <ncborch@gmail.com>
Date: Thu, 26 Sep 2024 09:38:18 -0500
Subject: [PATCH 2/2] v2.0.7

---
 DESCRIPTION | 2 +-
 NEWS.md     | 6 ++++++
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index aa4ca380..fa2d7193 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: scRepertoire
 Title: A toolkit for single-cell immune receptor profiling
-Version: 2.0.6
+Version: 2.0.7
 Authors@R: c(
     person(given = "Nick", family = "Borcherding", role = c("aut", "cre"), email = "ncborch@gmail.com"), 
     person(given = "Qile", family = "Yang", role = c("aut"), email = "qile.yang@berkeley.edu"), 
diff --git a/NEWS.md b/NEWS.md
index d1c32817..bcf67b14 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,9 @@
+# scRepertoire VERSION 2.0.7
+
+## UNDERLYING CHANGES
+* Fixed issue with "group.by" in ```clonalOverlap()```
+* Fixed issue with "group.by" in ```clonalCompare()```
+
 # scRepertoire VERSION 2.0.6
 
 ## UNDERLYING CHANGES