@@ -1,7 +1,7 @@

 Package: ggtree

 Type: Package

 Title: an R package for visualization of tree and annotation data

-Version: 3.5.1.902

+Version: 3.5.2

 Authors@R: c(

        person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), 

             comment = c(ORCID = "0000-0002-6485-8781")),

@@ -37,7 +37,8 @@ Imports:

     tidytree (>= 0.3.9),

     treeio (>= 1.8.0),

     utils,

-    scales

+    scales,

+    stats

 Suggests:

     emojifont,

     ggimage,

@@ -47,7 +48,6 @@ Suggests:

     knitr,

     prettydoc,

     rmarkdown,

-    stats,

     testthat,

     tibble,

     glue

@@ -62,5 +62,5 @@ BugReports: https://github.com/YuLab-SMU/ggtree/issues

 Packaged: 2014-12-03 08:16:14 UTC; root

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, Phylogenetics, ReproducibleResearch, Software, Visualization

-RoxygenNote: 7.2.0

+RoxygenNote: 7.2.1

 Roxygen: list(markdown = TRUE)

@@ -7,6 +7,7 @@ S3method(fortify,dendrogram)

 S3method(fortify,diana)

 S3method(fortify,hclust)

 S3method(fortify,igraph)

+S3method(fortify,linkage)

 S3method(fortify,multiPhylo)

 S3method(fortify,obkData)

 S3method(fortify,phylo)

@@ -268,6 +269,8 @@ importFrom(rlang,abort)

 importFrom(rlang,as_name)

 importFrom(rlang,quo_name)

 importFrom(scales,alpha)

+importFrom(stats,as.hclust)

+importFrom(stats,cutree)

 importFrom(tidyr,gather)

 importFrom(tidytree,MRCA)

 importFrom(tidytree,ancestor)

@@ -25,8 +25,10 @@

 -->

-# ggtree 3.5.1.902

+# ggtree 3.5.2

++ `scale_color_subtree()` now supports passing a numeric value and internally it will call `cutree(tree, k)` (2022-08-11, Thu)

++ support 'linkage' class defined in the 'mdendro' package (2022-08-11, Thu)

 + clone the plot environment before assigning layout (2022-07-19, Tue, #516)

 + bug fixed in 'equal_angle' layout (2022-07-08, Fri, #514)

 + optimize `geom_tiplab` to better compatible with dendrogram layout (2022-06-23, Thu, #508)

@@ -135,7 +135,8 @@ fortify.phylo4 <- function(model, data,

                            mrsd      = NULL,

                            hang      = .1,

                            ...) {

-    if (inherits(model, c("dendrogram", "agnes", "diana", "twins"))) {

+    if (inherits(model, c("dendrogram", "linkage", 

+                        "agnes", "diana", "twins"))) {

         model <- stats::as.hclust(model)

     }

@@ -190,6 +191,9 @@ fortify.phylog <- fortify.phylo4

 ##' @export

 fortify.igraph <- fortify.phylo4

+##' @method fortify linkage

+##' @export

+fortify.linkage <- fortify.phylo4

 ##' @method fortify phylo4d

 ##' @importFrom treeio as.treedata

@@ -10,7 +10,7 @@

 scale_color_subtree <- function(group) {

     if (inherits(group, 'kmeans')) {

         group <- group$cluster

-    }

+    } 

     structure(group,

               class = 'color_subtree'

@@ -18,10 +18,17 @@ scale_color_subtree <- function(group) {

 }

 ##' @rdname scale-color-subtree

+##' @importFrom stats as.hclust

+##' @importFrom stats cutree

 ##' @export

 scale_colour_subtree <- scale_color_subtree

-scale_color_subtree_ <- function(p, group) {    

+scale_color_subtree_ <- function(p, group) {

+

+    if (is.numeric(group) && length(group) == 1) {

+        group <- cutree(as.hclust(as.phylo(p$data)), group)

+    } 

+

     g <- split(names(group), group)

     groupOTU(p, g, group_name = 'subtree') +

         aes_(color = ~subtree)