agglomerateByRank: bugfix related to agglomeration non-existing tree (m…

…icrobiome#542)
Daenarys8 · May 13, 2024 · 7a0b0ea · 7a0b0ea
1 parent 13f7dce
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diff --git 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
@@ -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
@@ -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