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

 Package: ggtree

 Type: Package

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

-Version: 3.5.1.901

+Version: 3.5.2.992

 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

@@ -57,10 +57,10 @@ VignetteBuilder: knitr

 ByteCompile: true

 Encoding: UTF-8

 License: Artistic-2.0

-URL: https://yulab-smu.top/treedata-book/ (book), http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628 (paper)

+URL: https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/ (book), http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628 (paper)

 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)

@@ -24,11 +24,18 @@

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

 -->

+# ggtree 3.5.2.992

-# ggtree 3.5.1.901

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

++ add citation of the tree data book (2022-08-13, Sat)

+# 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)

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

 # ggtree 3.5.1

@@ -113,6 +113,9 @@ scale_x_range <- function() {

 ##' p2 + scale_x_continuous(labels=abs)

 ##' @author Guangchuang Yu

 revts <- function(treeview) {

+    if (!is.null(attr(treeview$data, 'revts.done'))){

+         return(treeview)

+    }

     x <- treeview$data$x

     mx <- max(x, na.rm=TRUE)

     treeview$data$x <- x - mx

@@ -32,6 +32,22 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

 }

+adjust_hclust_tip.edge.len <- function(df, phylo){

+    if (inherits(phylo, 'treedata')){

+        tip.edge.len <- attr(phylo@phylo, 'tip.edge.len')

+    }else{

+        tip.edge.len <- attr(phylo, 'tip.edge.len')

+    }

+    if (!is.null(tip.edge.len)){

+        mx <- max(df$x, na.rm=TRUE)

+        df$x <- df$x - mx

+        df$branch <- df$branch - mx

+        df[df$isTip, "x", drop=TRUE] <- tip.edge.len

+        attr(df, 'revts.done') = TRUE

+    }                       

+    return(df)

+}

+

 ##

 ##

 ## old version of fortify.phylo

@@ -205,6 +205,9 @@ GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,

         trans$curvature <- curvature

     }else{

         trans <- coord$transform(data, panel_params)

+        if (inherits(coord, 'CoordFlip')){ 

+            trans$curvature <- -1 * trans$curvature

+        }

     }

     arrow.fill <- arrow.fill %|||% trans$colour

@@ -226,6 +229,7 @@ GeomCurvelink <- ggproto("GeomCurvelink", GeomSegment,

   }

 )

+

 # for inward curve lines

 generate_curvature <- function(starttheta, endtheta, hratio, ncp){

     flag <- endtheta - starttheta

@@ -17,6 +17,9 @@

 ##' @param root.position position of the root node (default = 0)

 ##' @param xlim x limits, only works for 'inward_circular' layout

 ##' @param layout.params list, the parameters of layout, when layout is a function.

+##' @param hang numeric The fraction of the tree plot height by which labels should hang 

+##' below the rest of the plot. A negative value will cause the labels to hang down from 0. This

+##' parameter only work with the 'dendrogram' layout for 'hclust' like class, default is 0.1.

 ##' @return tree

 ##' @importFrom ggplot2 ggplot

 ##' @importFrom ggplot2 xlab

@@ -59,6 +62,7 @@ ggtree <- function(tr,

                    root.position  = 0,

                    xlim = NULL,

                    layout.params = list(),

+                   hang = .1,

                    ...) {

     # Check if layout string is valid.

@@ -102,6 +106,7 @@ ggtree <- function(tr,

                 right         = right,

                 branch.length = branch.length,

                 root.position = root.position,

+                hang          = hang,

                 ...)

     if (!is.null(dd)){

@@ -15,6 +15,7 @@

 rotate_tree <- function(treeview, angle) {

     treeview <- treeview + coord_polar(theta='y', start=(angle-90)/180*pi, -1)

     treeview$data$angle <- treeview$data$angle + angle

+    treeview$plot_env <- build_new_plot_env(treeview$plot_env)

     assign("layout", "circular", envir = treeview$plot_env)

     return(treeview)

 }

@@ -46,6 +47,7 @@ open_tree <- function(treeview, angle) {

     angle <- 360/(2+NN) * (1:N+1)

     angle <- angle[idx]

     p$data$angle <- angle

+    p$plot_env <- build_new_plot_env(p$plot_env)

     assign("layout", "fan", envir = p$plot_env)

     return(p)

 }

@@ -68,6 +68,7 @@ fortify.phylo <- function(model, data,

         res <- calculate_angle(res)

     }

     res <- scaleY(as.phylo(model), res, yscale, layout, ...)

+    res <- adjust_hclust_tip.edge.len(res, x)

     class(res) <- c("tbl_tree", class(res))

     attr(res, "layout") <- layout

     return(res)

@@ -133,13 +134,15 @@ fortify.phylo4 <- function(model, data,

                            ladderize = TRUE,

                            right     = FALSE,

                            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)

     }

     if (inherits(model, "hclust")) {

-        phylo <- as.phylo.hclust2(model)

+        phylo <- as.phylo.hclust2(model, hang = hang)

     } else {

         phylo <- as.phylo(model)

     }

@@ -181,6 +184,9 @@ fortify.phylog <- fortify.phylo4

 ##' @export

 fortify.igraph <- fortify.phylo4

+##' @method fortify linkage

+##' @export

+fortify.linkage <- fortify.phylo4

 ##' @method fortify phylo4d

 ##' @importFrom treeio as.treedata

@@ -192,8 +198,11 @@ fortify.phylo4d <- function(model, data,

                             right         = FALSE,

                             branch.length = "branch.length",

                             mrsd          = NULL,

+							hang          = 0.1,

                             ...) {

-    fortify(as.treedata(model), data, layout, yscale, ladderize, right, branch.length, mrsd, ...)

+    model <- as.treedata(model, hang = hang)

+    df <- fortify(model, data, layout, yscale, ladderize, right, branch.length, mrsd, ...)

+    return (df)

 }

 ##' @method fortify pvclust

@@ -100,7 +100,7 @@ ggplot_add.layout_ggtree <- function(object, plot, object_name) {

     if (object$layout == 'dendrogram') {

         plot <- revts(plot)

-        obj <- list(scale_x_reverse(labels = abs),

+        obj <- list(scale_x_reverse(labels = function(x){-x}),

                     coord_flip(clip = 'off')

                     )

     } else if (object$layout == 'circular' || object$layout == "inward_circular") {

@@ -115,8 +115,10 @@ ggplot_add.layout_ggtree <- function(object, plot, object_name) {

     } else { ## rectangular

         obj <- coord_cartesian(clip = 'off')

     }

+    plot <- ggplot_add(obj, plot, object_name)

+    plot$plot_env <- build_new_plot_env(plot$plot_env)

     assign("layout", object$layout, envir = plot$plot_env)

-    ggplot_add(obj, plot, object_name)

+    return(plot)

 }

@@ -200,8 +202,16 @@ ggplot_add.facet_plot <- function(object, plot, object_name) {

 ##' @export

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

     layout <- get_layout(plot)

-    if (layout == 'dendrogram' && object$hjust == 0 ){

-        object$hjust <- .5

+    if (layout == 'dendrogram'){

+        if( object$hjust == 0 ){

+            object$hjust = 1

+        }

+        if (!'vjust' %in% names(object)){

+            object$vjust = .5

+        }

+        if (!'angle' %in% names(object)){

+            object$angle = 90

+        }

     }

     if (object$as_ylab) {

         if (layout != "rectangular" && layout != "dendrogram") {

@@ -214,11 +224,11 @@ ggplot_add.tiplab <- function(object, plot, object_name) {

         ly <- do.call(geom_tiplab_rectangular, object)

         plot <- ggplot_add(ly, plot, object_name)

         object$size <- fontsize

-        object$mapping <- NULL

+        #object$mapping <- NULL

         object$align <- NULL

         object$linetype <- NULL

         object$linesize <- NULL

-        object$geom <- NULL

+        #object$geom <- NULL

         object$offset <- NULL

         object$nodelab <- NULL

         res <- ggplot_add.tiplab_ylab(object, plot, object_name)

@@ -249,11 +259,30 @@ ggplot_add.tiplab_ylab <- function(object, plot, object_name) {

     }

     df <- plot$data

-    df <- df[df$isTip, ]

+    if ('label' %in% names(object$mapping)){

+        if (object$geom == 'text'){

+            xx <- do.call('geom_text', list(mapping=object$mapping))

+            xx$computed_mapping <- c(xx$mapping, plot$mapping[setdiff(names(plot$mapping), names(xx$mapping))])

+            class(xx$computed_mapping) <- "uneval"

+            if (!is.null(object$data)){

+                df <- object$data

+            }else{

+                df <- df[df$isTip,]

+            }

+            df <- suppressWarnings(xx$compute_aesthetics(data=df, plot=plot))

+        }else{

+            message('The geom is not text, as_ylab will use original tip labels of tree')

+            df <- df[df$isTip, ]

+        }

+    }else{

+        df <- df[df$isTip, ]

+    }

     yscale <- scale_y_continuous(breaks = df$y, labels = df$label,

                                  position = object$position, expand = expansion(0, 0.6))

     object$position <- NULL

+    object$mapping <- NULL

+    object$geom <- NULL

     object$node <- NULL

     ytext <- do.call(element_text, object)

@@ -518,6 +547,9 @@ ggplot_add.hilight <- function(object, plot, object_name){

         if (flag_tbl_tree){

             object$data <-  object$data[,!colnames(object$data) %in% setdiff(flag_names, as_name(object$mapping$node)),drop=FALSE]

         }

+        object$data <- object$data[, !colnames(object$data) %in% setdiff(intersect(colnames(object$data), 

+                                                                     colnames(data)), 

+                                                                     as_name(object$mapping$node)), drop=FALSE]

         object$data <- merge(data, object$data, by.x="clade_root_node", by.y=as_name(object$mapping$node))

         object$data[[as_name(object$mapping$node)]] <- as.vector(object$data$clade_root_node)

         object$mapping <- object$mapping[!names(object$mapping) %in% c("node")]

@@ -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)

@@ -1355,14 +1355,21 @@ as.phylo.hclust2 <- function(x, hang=0.1, ...) {

     }

   }

-  len <- numeric(max(tr$edge))

-  len[nodes] <- h$height

-  pn <- ev[nodes]

-  pn[pn == 0] <- treeio::rootnode(tr)

-  len[nodes] <- len[pn] - len[nodes]

-  len[1:Ntip(tr)] <- hang #max(h$height)/10

-

-  tr$edge.length <- len[tr$edge[,2]]

+  #len <- numeric(max(tr$edge))

+  #len[nodes] <- h$height

+  #pn <- ev[nodes]

+  #pn[pn == 0] <- treeio::rootnode(tr)

+  #len[nodes] <- len[pn] - len[nodes]

+  #len[1:Ntip(tr)] <- hang #max(h$height)/10

+

+  #tr$edge.length <- len[tr$edge[,2]]

+

+  tip2parent <- tr$edge[match(seq_len(Ntip(tr)), tr$edge[,2]), 1]

+  if (hang > 0){

+    tip.edge.len <- hang * max(h$height) - h$height[match(tip2parent, nodes)]

+    attr(tr,'tip.edge.len') <- tip.edge.len

+  }

+  tr$edge.length <- tr$edge.length * 2

   return(tr)

 }

@@ -1,5 +1,4 @@

-

 ##' @importFrom ggplot2 last_plot

 get_tree_view <- function(tree_view) {

     if (is.null(tree_view))

@@ -17,6 +16,18 @@ get_layout <- function(tree_view = NULL) {

     return(layout)

 }

+build_new_plot_env <- function(env){

+    newenv <- list2env(

+                x = as.list(

+                  env, 

+                  all.names = TRUE

+                ), 

+                parent = parent.env(env)

+              )

+    attributes(newenv) <- attributes(env)

+    return(newenv)

+}

+

 reverse.treeview <- function(tv) {

     tv$data <- reverse.treeview.data(tv$data)

     return(tv)

@@ -1,5 +1,18 @@

 citHeader("To cite ggtree in publications use:")

+citEntry(

+    entry  = "book",

+    title = "Data Integration, Manipulation and Visualization of Phylogenetic Treess",

+    author = person("Guangchuang", "Yu"),

+	publisher = "Chapman and Hall/{CRC}",

+    year = "2022",

+	edition = "1st edition",

+    url = "https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/",

+    textVersion = paste("Guangchuang Yu. (2022).",

+                        "Data Integration, Manipulation and Visualization of Phylogenetic Trees (1st edition).",

+                        "Chapman and Hall/CRC.")   

+)

+

 citEntry(

     entry  = "article",

     title = "Using ggtree to Visualize Data on Tree-Like Structures",

@@ -22,6 +22,7 @@ ggtree(

   root.position = 0,

   xlim = NULL,

   layout.params = list(),

+  hang = 0.1,

   ...

 )

 }

@@ -57,6 +58,10 @@ right-hand side? See \code{\link[ape:ladderize]{ape::ladderize()}} for more info

 \item{layout.params}{list, the parameters of layout, when layout is a function.}

+\item{hang}{numeric The fraction of the tree plot height by which labels should hang

+below the rest of the plot. A negative value will cause the labels to hang down from 0. This

+parameter only work with the 'dendrogram' layout for 'hclust' like class, default is 0.1.}

+

 \item{...}{additional parameter

 some dot arguments: