From 7a0b0ead9d82087f86e29e4867b3412f88303cd7 Mon Sep 17 00:00:00 2001
From: Tuomas Borman <60338854+TuomasBorman@users.noreply.github.com>
Date: Mon, 13 May 2024 14:32:31 +0300
Subject: [PATCH] agglomerateByRank: bugfix related to agglomeration
 non-existing tree (#542)

---
 DESCRIPTION     | 2 +-
 NEWS            | 1 +
 R/agglomerate.R | 7 +++----
 3 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a4ac31c39..d5ba7ee2d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: mia
 Type: Package
-Version: 1.13.3
+Version: 1.13.4
 Authors@R:
     c(person(given = "Felix G.M.", family = "Ernst", role = c("aut"),
              email = "felix.gm.ernst@outlook.com",
diff --git a/NEWS b/NEWS
index b72e7755f..da9ee40d2 100644
--- a/NEWS
+++ b/NEWS
@@ -117,3 +117,4 @@ Changes in version 1.13.x
 + Added new functions getMediation and addMediation
 + replace getExperiment* and testExperiment* functions with getCrossAssociation
 + Replace mergeRows and mergeCols with new function agglomerateByVariable
++ agglomerateByRank: bugfix related to agglomeration of non-existing tree
diff --git a/R/agglomerate.R b/R/agglomerate.R
index ac2026477..d03a30f35 100644
--- a/R/agglomerate.R
+++ b/R/agglomerate.R
@@ -371,10 +371,9 @@ setMethod(
                 }
                 # Agglomerate data
                 x <- callNextMethod(x, ...)
-                # Agglomerate also tree, if the data includes only one
-                # rowTree --> otherwise it is not possible to agglomerate
-                # since all rownames are not found from individual tree.
-                if(agglomerate.tree){
+                # Agglomerate also trees if user has specified and if there
+                # are trees available
+                if( agglomerate.tree && !is.null(x@rowTree) ){
                     x <- .agglomerate_trees(x)
                 }
                 x