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

 Package: ggtree

 Type: Package

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

-Version: 3.5.3

+Version: 3.5.3.001

 Authors@R: c(

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

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

@@ -21,7 +21,6 @@ S3method(fortify,treedataList)

 S3method(fortify,twins)

 S3method(ggplot_add,cladelab)

 S3method(ggplot_add,cladelabel)

-S3method(ggplot_add,color_subtree)

 S3method(ggplot_add,facet_plot)

 S3method(ggplot_add,facet_xlim)

 S3method(ggplot_add,geom_range)

@@ -269,8 +268,6 @@ 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)

@@ -24,6 +24,11 @@

   - <https://github.com/thomasp85/ggraph/commit/14de66f1225336179b4598cb42a4beda95682211>

 -->

+

+# ggtree 3.5.3.001

+

++ move `scale_color_subtree()` to the 'ggtreeDendro' package (2022-09-23, Fri)

+

 # ggtree 3.5.3

 + update `fortify` method for `pvclust` object (2022-08-15, Mon)

@@ -1,3 +1,25 @@

+## defunct since v=3.5.3

+

+##' scale tree color by subtree (e.g., output of cutree, kmeans, or other clustering algorithm)

+##'

+##' 

+##' @title scale_color_subtree

+##' @rdname scale-color-subtree

+##' @param group taxa group information

+##' @return updated tree view

+##' @export

+##' @author Guangchuang Yu

+scale_color_subtree <- function(group) {

+    message("This scale function was moved to the ggtreeDendro package\n",

+        "please use 'ggtreeDendro::scale_color_subtree' instead.\n")

+    NULL

+}

+

+##' @rdname scale-color-subtree

+##' @export

+scale_colour_subtree <- scale_color_subtree

+

+

 ## ##' annotation taxa with images

 ## ##'

 ## ##'

@@ -174,11 +174,7 @@ ggexpand_internal <- function(plot, ratio, direction, var) {

     return(res)

 }

-##' @method ggplot_add color_subtree

-##' @export

-ggplot_add.color_subtree <- function(object, plot, object_name) {

-    scale_color_subtree_(plot, object)

-}

+

 ##' @method ggplot_add tree_inset

 ##' @export

@@ -1,38 +1,4 @@

-##' scale tree color by subtree (e.g., output of cutree, kmeans, or other clustering algorithm)

-##'

-##' 

-##' @title scale_color_subtree

-##' @rdname scale-color-subtree

-##' @param group taxa group information

-##' @return updated tree view

-##' @export

-##' @author Guangchuang Yu

-scale_color_subtree <- function(group) {

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

-        group <- group$cluster

-    } 

-

-    structure(group,

-              class = 'color_subtree'

-              )

-}

-##' @rdname scale-color-subtree

-##' @importFrom stats as.hclust

-##' @importFrom stats cutree

-##' @export

-scale_colour_subtree <- scale_color_subtree

-

-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)

-}

 ##' scale color by a numerical tree attribute

 ##'

@@ -1,5 +1,5 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/method-scale-color.R

+% Please edit documentation in R/defunct.R

 \name{scale_color_subtree}

 \alias{scale_color_subtree}

 \alias{scale_colour_subtree}