@@ -162,8 +162,13 @@ recodeClusterZ <- function(sce, from, to, altExpName = "featureSubset") {

         stop("Provided 'sce' argument does not have a 'celda_cell_cluster'",

             " column in 'colData(altExp(sce, altExpName))'")

     }

-    celdaClusters(sce, altExpName = altExpName) <- plyr::mapvalues(

-        celdaClusters(sce, altExpName = altExpName), from, to)

+    new.clusters <- plyr::mapvalues(celdaClusters(sce,

+                                                  altExpName = altExpName),

+                                    from, to)

+    new.clusters <- factor(new.clusters, levels = 

+                             sort(as.numeric(unique(new.clusters))))

+    

+    celdaClusters(sce, altExpName = altExpName) <- new.clusters

     return(sce)

 }

@@ -210,6 +215,12 @@ recodeClusterY <- function(sce, from, to, altExpName = "featureSubset") {

         stop("Provided 'sce' argument does not have a 'celda_feature_module'",

             " column in 'rowData(altExp(sce, altExpName))'")

     }

+    new.clusters <- plyr::mapvalues(celdaModules(sce,

+                                                  altExpName = altExpName),

+                                  from, to)

+    new.clusters <- factor(new.clusters, levels = 

+                             sort(as.numeric(unique(new.clusters))))

+  

     celdaModules(sce, altExpName = altExpName) <- plyr::mapvalues(

         celdaModules(sce, altExpName = altExpName), from, to)

     return(sce)