@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.13.2

+Version: 1.13.3

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),

@@ -51,4 +51,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues

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

 biocViews: Alignment, Annotation, Clustering, DataImport,

     MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization

-RoxygenNote: 6.0.1

+RoxygenNote: 6.1.0

@@ -1,3 +1,8 @@

+# ggtree 1.13.3

+

++ update `viewClade` according to the change of `ggplot2` (2018-08-07, Tue)

+  - <https://github.com/GuangchuangYu/ggtree/issues/188>

+  

 # ggtree 1.13.2

 + xmax_adjust  in `viewClade` (2018-07-21, Sat)

@@ -40,7 +40,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     ## xd <- tree_view$data$branch.length[node]/2

     cpos <- get_clade_position(tree_view, node=node)

-    xmax <- ggplot_build(tree_view)$layout$panel_ranges[[1]]$x.range[2]

+    xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2]

     attr(tree_view, 'viewClade') <- TRUE

     attr(tree_view, 'viewClade_node') <- node

@@ -6,8 +6,8 @@

 \usage{

 geom_cladelabel(node, label, offset = 0, offset.text = 0, extend = 0,

   align = FALSE, barsize = 0.5, fontsize = 3.88, angle = 0,

-  geom = "text", hjust = 0, color = NULL, fill = NA, family = "sans",

-  parse = FALSE, ...)

+  geom = "text", hjust = 0, color = NULL, fill = NA,

+  family = "sans", parse = FALSE, ...)

 }

 \arguments{

 \item{node}{selected node}

@@ -4,9 +4,10 @@

 \alias{geom_cladelabel2}

 \title{geom_cladelabel2}

 \usage{

-geom_cladelabel2(node, label, offset = 0, offset.text = 0, offset.bar = 0,

-  align = FALSE, barsize = 0.5, fontsize = 3.88, hjust = 0,

-  geom = "text", color = NULL, family = "sans", parse = FALSE, ...)

+geom_cladelabel2(node, label, offset = 0, offset.text = 0,

+  offset.bar = 0, align = FALSE, barsize = 0.5, fontsize = 3.88,

+  hjust = 0, geom = "text", color = NULL, family = "sans",

+  parse = FALSE, ...)

 }

 \arguments{

 \item{node}{selected node}

@@ -5,10 +5,10 @@

 \title{geom_label2}

 \usage{

 geom_label2(mapping = NULL, data = NULL, ..., stat = "identity",

-  position = "identity", family = "sans", parse = FALSE, nudge_x = 0,

-  nudge_y = 0, label.padding = unit(0.25, "lines"), label.r = unit(0.15,

-  "lines"), label.size = 0.25, na.rm = TRUE, show.legend = NA,

-  inherit.aes = TRUE)

+  position = "identity", family = "sans", parse = FALSE,

+  nudge_x = 0, nudge_y = 0, label.padding = unit(0.25, "lines"),

+  label.r = unit(0.15, "lines"), label.size = 0.25, na.rm = TRUE,

+  show.legend = NA, inherit.aes = TRUE)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -4,8 +4,8 @@

 \alias{geom_nodelab}

 \title{geom_nodelab}

 \usage{

-geom_nodelab(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text",

-  hjust = 0.5, ...)

+geom_nodelab(mapping = NULL, nudge_x = 0, nudge_y = 0,

+  geom = "text", hjust = 0.5, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -4,8 +4,8 @@

 \alias{geom_nodelab2}

 \title{@geom_nodelab2}

 \usage{

-geom_nodelab2(mapping = NULL, nudge_x = 0, nudge_y = 0, geom = "text",

-  hjust = 0.5, ...)

+geom_nodelab2(mapping = NULL, nudge_x = 0, nudge_y = 0,

+  geom = "text", hjust = 0.5, ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -4,7 +4,8 @@

 \alias{geom_range}

 \title{geom_range}

 \usage{

-geom_range(range = "length_0.95_HPD", branch.length = "branch.length", ...)

+geom_range(range = "length_0.95_HPD", branch.length = "branch.length",

+  ...)

 }

 \arguments{

 \item{range}{range, e.g. "height_0.95_HPD"}

@@ -5,9 +5,9 @@

 \title{geom_strip}

 \usage{

 geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0,

-  align = TRUE, barsize = 0.5, extend = 0, fontsize = 3.88, angle = 0,

-  geom = "text", hjust = 0, fill = NA, family = "sans", parse = FALSE,

-  ...)

+  align = TRUE, barsize = 0.5, extend = 0, fontsize = 3.88,

+  angle = 0, geom = "text", hjust = 0, fill = NA,

+  family = "sans", parse = FALSE, ...)

 }

 \arguments{

 \item{taxa1}{taxa1}

@@ -5,9 +5,9 @@

 \title{geom_text2}

 \usage{

 geom_text2(mapping = NULL, data = NULL, ..., stat = "identity",

-  position = "identity", family = "sans", parse = FALSE, na.rm = TRUE,

-  show.legend = NA, inherit.aes = TRUE, nudge_x = 0, nudge_y = 0,

-  check_overlap = FALSE)

+  position = "identity", family = "sans", parse = FALSE,

+  na.rm = TRUE, show.legend = NA, inherit.aes = TRUE, nudge_x = 0,

+  nudge_y = 0, check_overlap = FALSE)

 }

 \arguments{

 \item{mapping}{the aesthetic mapping}

@@ -5,7 +5,8 @@

 \title{geom_tiplab}

 \usage{

 geom_tiplab(mapping = NULL, hjust = 0, align = FALSE,

-  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0, ...)

+  linetype = "dotted", linesize = 0.5, geom = "text", offset = 0,

+  ...)

 }

 \arguments{

 \item{mapping}{aes mapping}

@@ -5,7 +5,8 @@

 \title{geom_treescale}

 \usage{

 geom_treescale(x = NULL, y = NULL, width = NULL, offset = NULL,

-  color = "black", linesize = 0.5, fontsize = 3.88, family = "sans")

+  color = "black", linesize = 0.5, fontsize = 3.88,

+  family = "sans")

 }

 \arguments{

 \item{x}{x position}

@@ -5,13 +5,13 @@

 \alias{ggtree}

 \alias{package-ggtree}

 \alias{ggtree-package}

-\alias{ggtree}

 \title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics

 \code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}

 \usage{

 ggtree(tr, mapping = NULL, layout = "rectangular", open.angle = 0,

-  mrsd = NULL, as.Date = FALSE, yscale = "none", yscale_mapping = NULL,

-  ladderize = TRUE, right = FALSE, branch.length = "branch.length", ...)

+  mrsd = NULL, as.Date = FALSE, yscale = "none",

+  yscale_mapping = NULL, ladderize = TRUE, right = FALSE,

+  branch.length = "branch.length", ...)

 }

 \arguments{

 \item{tr}{phylo object}

@@ -4,9 +4,10 @@

 \alias{gheatmap}

 \title{gheatmap}

 \usage{

-gheatmap(p, data, offset = 0, width = 1, low = "green", high = "red",

-  color = "white", colnames = TRUE, colnames_position = "bottom",

-  colnames_angle = 0, colnames_level = NULL, colnames_offset_x = 0,

+gheatmap(p, data, offset = 0, width = 1, low = "green",

+  high = "red", color = "white", colnames = TRUE,

+  colnames_position = "bottom", colnames_angle = 0,

+  colnames_level = NULL, colnames_offset_x = 0,

   colnames_offset_y = 0, font.size = 4, hjust = 0.5)

 }

 \arguments{

@@ -3,7 +3,6 @@

 \docType{methods}

 \name{gzoom}

 \alias{gzoom}

-\alias{gzoom}

 \alias{gzoom,ggtree-method}

 \alias{gzoom,treedata-method}

 \alias{gzoom,phylo-method}

@@ -14,8 +13,8 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 \S4method{gzoom}{ggtree}(object, focus, widths = c(0.3, 0.7),

   xmax_adjust = 0)

-\S4method{gzoom}{treedata}(object, focus, subtree = FALSE, widths = c(0.3,

-  0.7))

+\S4method{gzoom}{treedata}(object, focus, subtree = FALSE,

+  widths = c(0.3, 0.7))

 \S4method{gzoom}{phylo}(object, focus, subtree = FALSE, widths = c(0.3,

   0.7))

@@ -37,5 +36,9 @@ gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...)

 figure

 }

 \description{

+gzoom method

+

+gzoom method

+

 zoom selected subtree

 }

@@ -4,8 +4,8 @@

 \alias{inset}

 \title{inset}

 \usage{

-inset(tree_view, insets, width, height, hjust = 0, vjust = 0, x = "node",

-  reverse_x = FALSE, reverse_y = FALSE)

+inset(tree_view, insets, width, height, hjust = 0, vjust = 0,

+  x = "node", reverse_x = FALSE, reverse_y = FALSE)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -4,8 +4,8 @@

 \alias{msaplot}

 \title{msaplot}

 \usage{

-msaplot(p, fasta, offset = 0, width = 1, color = NULL, window = NULL,

-  bg_line = TRUE, height = 0.8)

+msaplot(p, fasta, offset = 0, width = 1, color = NULL,

+  window = NULL, bg_line = TRUE, height = 0.8)

 }

 \arguments{

 \item{p}{tree view}

@@ -4,8 +4,8 @@

 \alias{phylopic}

 \title{phylopic}

 \usage{

-phylopic(tree_view, phylopic_id, size = 512, color = "black", alpha = 0.5,

-  node = NULL, x = NULL, y = NULL, width = 0.1)

+phylopic(tree_view, phylopic_id, size = 512, color = "black",

+  alpha = 0.5, node = NULL, x = NULL, y = NULL, width = 0.1)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -4,67 +4,35 @@

 \name{reexports}

 \alias{reexports}

 \alias{rtree}

-\alias{reexports}

 \alias{read.tree}

-\alias{reexports}

 \alias{read.nexus}

-\alias{reexports}

 \alias{groupOTU}

-\alias{reexports}

 \alias{groupClade}

-\alias{reexports}

 \alias{collapse}

-\alias{reexports}

 \alias{fortify}

-\alias{reexports}

 \alias{ggplot}

-\alias{reexports}

 \alias{xlim}

-\alias{reexports}

 \alias{theme}

-\alias{reexports}

 \alias{ggsave}

-\alias{reexports}

 \alias{aes}

-\alias{reexports}

-\alias{fortify}

-\alias{reexports}

 \alias{geom_text}

-\alias{reexports}

 \alias{geom_label}

-\alias{reexports}

 \alias{geom_point}

-\alias{reexports}

 \alias{read.astral}

-\alias{reexports}

 \alias{read.beast}

-\alias{reexports}

 \alias{read.codeml}

-\alias{reexports}

 \alias{read.codeml_mlc}

-\alias{reexports}

 \alias{read.hyphy}

-\alias{reexports}

 \alias{read.iqtree}

-\alias{reexports}

 \alias{read.jplace}

-\alias{reexports}

 \alias{read.jtree}

-\alias{reexports}

 \alias{read.mrbayes}

-\alias{reexports}

 \alias{read.newick}

-\alias{reexports}

 \alias{read.nhx}

-\alias{reexports}

 \alias{read.paml_rst}

-\alias{reexports}

 \alias{read.phylip}

-\alias{reexports}

 \alias{read.phyloT}

-\alias{reexports}

 \alias{read.r8s}

-\alias{reexports}

 \alias{read.raxml}

 \title{Objects exported from other packages}

 \keyword{internal}

@@ -21,5 +21,7 @@ reroot(object, node, ...)

 tree object

 }

 \description{

+reroot method

+

 reroot a tree

 }

@@ -24,5 +24,7 @@ scale_color(object, by, ...)

 color vector

 }

 \description{

+scale_color method

+

 scale color by a numerical tree attribute

 }