@@ -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: 1.7.10

+Version: 1.7.11

 Authors@R: c(

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

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

@@ -1,3 +1,9 @@

+CHANGES IN VERSION 1.7.11

+------------------------

+ o remove layout.method parameter <2017-04-20, Thu>

+   + https://github.com/GuangchuangYu/ggtree/issues/118#issuecomment-295130818

+   + https://github.com/GuangchuangYu/ggtree/issues/125

+

 CHANGES IN VERSION 1.7.10

 ------------------------

  o add message for subview, inset, phylopic, theme_transparent and theme_inset <2017-03-23, Thu>

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

 ##' @title geom_tree

 ##' @param mapping aesthetic mapping

 ##' @param data data

-##' @param layout one of 'rectangular', 'slanted', 'circular', 'radial' or 'unrooted'

+##' @param layout one of 'rectangular', 'slanted', 'circular', 'radial', 'equal_angle' or 'daylight'

 ##' @param multiPhylo logical

 ##' @param ... additional parameter

 ##' @return tree layer

@@ -61,7 +61,7 @@ stat_tree <- function(mapping=NULL, data=NULL, geom="segment", position="identit

                    check.aes = FALSE

                    )

              )

-    } else if (layout %in% c("slanted", "radial", "unrooted")) {

+    } else if (layout %in% c("slanted", "radial", "equal_angle", "daylight")) {

         layer(stat=StatTree,

               data=data,

               mapping=mapping,

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

 ##' @title ggtree

 ##' @param tr phylo object

 ##' @param mapping aes mapping

-##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'

-##' @param layout.method of 'equal_angle', 'daylight'.

+##' @param layout one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'

 ##' @param open.angle open angle, only for 'fan' layout

 ##' @param mrsd most recent sampling date

 ##' @param as.Date logical whether using Date class in time tree

@@ -34,7 +33,6 @@

 ggtree <- function(tr,

                    mapping        = NULL,

                    layout         = "rectangular",

-                   layout.method  = "equal_angle",

                    open.angle     = 0,

                    mrsd           = NULL,

                    as.Date        = FALSE,

@@ -47,9 +45,12 @@ ggtree <- function(tr,

                    ...) {

     # Check if layout string is valid.

-    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))

-    layout.method %<>% match.arg(c("equal_angle", "daylight"))

-  

+    layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted", "equal_angle", "daylight"))

+    if (layout == "unrooted") {

+        layout <- "daylight"

+        message('"daylight" method was used as default layout for unrooted tree.')

+    }

+

     if (is(tr, "r8s") && branch.length == "branch.length") {

         branch.length = "TREE"

     }

@@ -64,11 +65,10 @@ ggtree <- function(tr,

     } else {

         mapping <- modifyList(aes_(~x, ~y), mapping)

     }

-  

-    p <- ggplot(tr, 

+

+    p <- ggplot(tr,

                 mapping       = mapping,

                 layout        = layout,

-                layout.method = layout.method,

                 mrsd          = mrsd,

                 as.Date       = as.Date,

                 yscale        = yscale,

@@ -110,7 +110,6 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

 ##' @export

 fortify.beast <- function(model, data,

                           layout        = "rectangular",

-                          layout.method = "equal_angle",

                           yscale        = "none",

                           ladderize     = TRUE,

                           right         = FALSE,

@@ -120,9 +119,12 @@ fortify.beast <- function(model, data,

     model <- set_branch_length(model, branch.length)

     phylo <- model@phylo

-    df    <- fortify(phylo, layout=layout, layout.method=layout.method,

-                     branch.length=branch.length,

-                     ladderize=ladderize, right=right, mrsd = mrsd, ...)

+    df    <- fortify(phylo,

+                     layout = layout,

+                     branch.length = branch.length,

+                     ladderize = ladderize,

+                     right = right,

+                     mrsd = mrsd, ...)

     stats <- model@stats

@@ -222,7 +224,6 @@ fortify.beast <- function(model, data,

 ##' @export

 fortify.codeml <- function(model, data,

                            layout        = "rectangular",

-                           layout.method = "equal_angle",

                            yscale        = "none",

                            ladderize     = TRUE,

                            right         = FALSE,

@@ -268,7 +269,6 @@ fortify.codeml <- function(model, data,

 ##' @export

 fortify.codeml_mlc <- function(model, data,

                                layout        = "rectangular",

-                               layout.method = "equal_angle",

                                yscale        = "none",

                                ladderize     = TRUE,

                                right         = FALSE,

@@ -310,7 +310,6 @@ merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

 fortify.codeml_mlc_ <- function(model, data,

                                 layout        = "rectangular",

-                                layout.method = "equal_angle",

                                 ladderize     = TRUE,

                                 right         = FALSE,

                                 branch.length = "branch.length",

@@ -322,12 +321,13 @@ fortify.codeml_mlc_ <- function(model, data,

 ##' @method fortify paml_rst

 ##' @export

-fortify.paml_rst <- function(model, data, 

-                             layout = "rectangular", 

-                             yscale="none",

-                             ladderize=TRUE, 

-                             right=FALSE, 

-                             mrsd=NULL, ...) {

+fortify.paml_rst <- function(model, data,

+                             layout    = "rectangular",

+                             yscale    = "none",

+                             ladderize = TRUE,

+                             right     = FALSE,

+                             mrsd      = NULL,

+                             ...) {

     df <- fortify.phylo(model@phylo, data, layout, ladderize, right, mrsd=mrsd, ...)

     df <- merge_phylo_anno.paml_rst(df, model)

     df <- scaleY(model@phylo, df, yscale, layout, ...)

@@ -362,11 +362,12 @@ fortify.hyphy <- fortify.paml_rst

 ##' @importFrom treeio get.placements

 ##' @export

 fortify.jplace <- function(model, data,

-                           layout="rectangular",

-                           yscale="none",

-                           ladderize=TRUE, 

-                           right=FALSE, 

-                           mrsd=NULL, ...) {

+                           layout    = "rectangular",

+                           yscale    = "none",

+                           ladderize = TRUE,

+                           right     = FALSE,

+                           mrsd      = NULL,

+                           ...) {

     df <- extract.treeinfo.jplace(model, layout, ladderize, right, mrsd=mrsd, ...)

     place <- get.placements(model, by="best")

@@ -405,8 +406,13 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

 ##' @method fortify phylo4

 ##' @importFrom treeio as.phylo

 ##' @export

-fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none",

-                           ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

+fortify.phylo4 <- function(model, data,

+                           layout    = "rectangular",

+                           yscale    = "none",

+                           ladderize = TRUE,

+                           right     = FALSE,

+                           mrsd      = NULL,

+                           ...) {

     phylo <- as.phylo(model)

     df <- fortify.phylo(phylo, data,

                         layout, ladderize, right, mrsd=mrsd, ...)

@@ -415,14 +421,14 @@ fortify.phylo4 <- function(model, data, layout="rectangular", yscale="none",

 ##' @method fortify phylo4d

 ##' @export

-fortify.phylo4d <- function(model, data, 

-                            layout="rectangular",

-                            layout.method = "equal_angle",

-                            yscale="none",

-                            ladderize=TRUE, 

-                            right=FALSE, 

-                            branch.length="branch.length",

-                            mrsd=NULL, ...) {

+fortify.phylo4d <- function(model, data,

+                            layout        = "rectangular",

+                            yscale        = "none",

+                            ladderize     = TRUE,

+                            right         = FALSE,

+                            branch.length = "branch.length",

+                            mrsd          = NULL,

+                            ...) {

     ## model <- set_branch_length(model, branch.length)

     ## phylo <- as.phylo.phylo4(model)

     ## res <- fortify(phylo, data, layout, branch.length=branch.length,

@@ -430,7 +436,7 @@ fortify.phylo4d <- function(model, data,

     ## tdata <- model@data[match(res$node, rownames(model@data)), , drop=FALSE]

     ## df <- cbind(res, tdata)

     ## scaleY(as.phylo.phylo4(model), df, yscale, layout, ...)

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

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

 }

@@ -455,12 +461,12 @@ fortify.phylo4d <- function(model, data,

 ##' @method fortify phylo

 ##' @export

 ##' @author Yu Guangchuang

-fortify.phylo <- function(model, data, 

-                          layout="rectangular",

-                          ladderize=TRUE, 

-                          right=FALSE, 

-                          mrsd=NULL, 

-                          as.Date=FALSE, ...) {

+fortify.phylo <- function(model, data,

+                          layout    = "rectangular",

+                          ladderize = TRUE,

+                          right     = FALSE,

+                          mrsd      = NULL,

+                          as.Date   = FALSE, ...) {

     tree <- reorder.phylo(model, 'postorder')

     if (ladderize == TRUE) {

@@ -516,8 +522,8 @@ fortify.phylo <- function(model, data,

 ##' @author Yu Guangchuang

 as.data.frame.phylo <- function(x, row.names, optional,

                                 layout="rectangular", ...) {

-    if (layout == "unrooted") {

-        return(layout.unrooted(x, ...))

+    if (layout %in% c("equal_angle", "daylight")) {

+        return(layout.unrooted(x, layout.method = layout, ...))

     }

     as.data.frame.phylo_(x, layout, ...)

 }

@@ -605,8 +611,11 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

 ##' @method fortify multiPhylo

 ##' @export

-fortify.multiPhylo <-  function(model, data, layout="rectangular",

-                                ladderize=TRUE, right=FALSE, mrsd=NULL, ...) {

+fortify.multiPhylo <-  function(model, data,

+                                layout    = "rectangular",

+                                ladderize = TRUE,

+                                right     = FALSE,

+                                mrsd      = NULL, ...) {

     df.list <- lapply(model, function(x) fortify(x, layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...))

     if (is.null(names(model))) {

@@ -626,26 +635,24 @@ fortify.multiPhylo <-  function(model, data, layout="rectangular",

 ##' @method fortify phylip

 ##' @export

-fortify.phylip <- function(model, data, 

-                           layout="rectangular",

-                           layout.method = "equal_angle",

-                           ladderize=TRUE, 

-                           right=FALSE,

-                           branch.length = "TREE", 

-                           mrsd=NULL, ...) {

+fortify.phylip <- function(model, data,

+                           layout        = "rectangular",

+                           ladderize     = TRUE,

+                           right         = FALSE,

+                           branch.length = "TREE",

+                           mrsd          = NULL, ...) {

     trees <- get.tree(model)

     fortify(trees, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)

 }

 ##' @method fortify r8s

 ##' @export

-fortify.r8s <- function(model, data, 

-                        layout="rectangular",

-                        layout.method = "equal_angle",

-                        ladderize=TRUE, 

-                        right=FALSE,

-                        branch.length = "TREE", 

-                        mrsd=NULL, ...) {

+fortify.r8s <- function(model, data,

+                        layout        = "rectangular",

+                        ladderize     = TRUE,

+                        right         = FALSE,

+                        branch.length = "TREE",

+                        mrsd          = NULL, ...) {

     trees <- get.tree(model)

     branch.length %<>% match.arg(names(trees))

     phylo <- trees[[branch.length]]

@@ -654,11 +661,11 @@ fortify.r8s <- function(model, data,

 ##' @method fortify obkData

 ##' @export

-fortify.obkData <- function(model, data, 

-                            layout="rectangular",

-                            ladderize=TRUE, 

-                            right=FALSE, 

-                            mrsd = NULL, ...) {

+fortify.obkData <- function(model, data,

+                            layout    = "rectangular",

+                            ladderize = TRUE,

+                            right     = FALSE,

+                            mrsd      = NULL, ...) {

     df <- fortify(model@trees[[1]], layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

@@ -676,11 +683,11 @@ fortify.obkData <- function(model, data,

 ##' @method fortify phyloseq

 ##' @export

-fortify.phyloseq <- function(model, data, 

-                             layout="rectangular",

-                             ladderize=TRUE, 

-                             right=FALSE, 

-                             mrsd=NULL, ...) {

+fortify.phyloseq <- function(model, data,

+                             layout    = "rectangular",

+                             ladderize = TRUE,

+                             right     = FALSE,

+                             mrsd      = NULL, ...) {

     df <- fortify(model@phy_tree, layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

     phyloseq <- "phyloseq"

@@ -180,80 +180,80 @@ layout.unrooted <- function(tree, branch.length="branch.length", layout.method="

 ##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.

 ##' @return tree as data.frame with equal angle layout.

 layoutEqualAngle <- function(tree, branch.length ){

-  root <- getRoot(tree)

-  # Convert Phylo tree to data.frame.

-  df <- as.data.frame.phylo_(tree)

-

-  # NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

-

-  # create and assign NA to the following fields.

-  df$x <- NA

-  df$y <- NA

-  df$start <- NA # Start angle of segment of subtree.

-  df$end   <- NA # End angle of segment of subtree

-  df$angle <- NA # Orthogonal angle to beta ... for labels??

-  # Initialize root node position and angles.

-  df[root, "x"] <- 0

-  df[root, "y"] <- 0

-  df[root, "start"] <- 0 # 0-degrees

-  df[root, "end"]   <- 2 # 360-degrees

-  df[root, "angle"] <- 0 # Angle label.

-

-  N <- getNodeNum(tree)

-

-  # Get number of tips for each node in tree.

-  nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

-  # Get list of node id's.

-  nodes <- getNodes_by_postorder(tree)

-

-  for(curNode in nodes) {

-    # Get number of tips for current node.

-    curNtip <- nb.sp[curNode]

-    # Get array of child node indexes of current node.

-    children <- getChild(tree, curNode)

-

-    # Get "start" and "end" angles of a segment for current node in the data.frame.

-    start <- df[curNode, "start"]

-    end <- df[curNode, "end"]

+    root <- getRoot(tree)

+    ## Convert Phylo tree to data.frame.

+    df <- as.data.frame.phylo_(tree)

+

+    ## NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

+

+    ## create and assign NA to the following fields.

+    df$x <- NA

+    df$y <- NA

+    df$start <- NA # Start angle of segment of subtree.

+    df$end   <- NA # End angle of segment of subtree

+    df$angle <- NA # Orthogonal angle to beta ... for labels??

+    ## Initialize root node position and angles.

+    df[root, "x"] <- 0

+    df[root, "y"] <- 0

+    df[root, "start"] <- 0 # 0-degrees

+    df[root, "end"]   <- 2 # 360-degrees

+    df[root, "angle"] <- 0 # Angle label.

+

+    N <- getNodeNum(tree)

+

+    ## Get number of tips for each node in tree.

+    nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

+    ## Get list of node id's.

+    nodes <- getNodes_by_postorder(tree)

+

+    for(curNode in nodes) {

+        ## Get number of tips for current node.

+        curNtip <- nb.sp[curNode]

+        ## Get array of child node indexes of current node.

+        children <- getChild(tree, curNode)

+

+        ## Get "start" and "end" angles of a segment for current node in the data.frame.

+        start <- df[curNode, "start"]

+        end <- df[curNode, "end"]

+

+        if (length(children) == 0) {

+            ## is a tip

+            next

+        }

-    if (length(children) == 0) {

-      ## is a tip

-      next

-    }

+        for (i in seq_along(children)) {

+            child <- children[i]

+            ## Get the number of tips for child node.

+            ntip.child <- nb.sp[child]

+

+            ## Calculated in half radians.

+            ## alpha: angle of segment for i-th child with ntips_ij tips.

+            ## alpha = (left_angle - right_angle) * (ntips_ij)/(ntips_current)

+            alpha <- (end - start) * ntip.child / curNtip

+            ## beta = angle of line from parent node to i-th child.

+            beta <- start + alpha / 2

+

+            if (branch.length == "none") {

+                length.child <- 1

+            } else {

+                length.child <- df[child, "length"]

+            }

-    for (i in seq_along(children)) {

-      child <- children[i]

-      # Get the number of tips for child node.

-      ntip.child <- nb.sp[child]

-

-      # Calculated in half radians.

-      # alpha: angle of segment for i-th child with ntips_ij tips.

-      # alpha = (left_angle - right_angle) * (ntips_ij)/(ntips_current)

-      alpha <- (end - start) * ntip.child / curNtip

-      # beta = angle of line from parent node to i-th child.

-      beta <- start + alpha / 2

-

-      if (branch.length == "none") {

-        length.child <- 1

-      } else {

-        length.child <- df[child, "length"]

-      }

+            ## update geometry of data.frame.

+            ## Calculate (x,y) position of the i-th child node from current node.

+            df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

+            df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

+            ## Calculate orthogonal angle to beta.

+            df[child, "angle"] <- -90 - 180 * beta * sign(beta - 1)

+            ## Update the start and end angles of the childs segment.

+            df[child, "start"] <- start

+            df[child, "end"] <- start + alpha

+            start <- start + alpha

+        }

-      # update geometry of data.frame.

-      # Calculate (x,y) position of the i-th child node from current node.

-      df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

-      df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

-      # Calculate orthogonal angle to beta.

-      df[child, "angle"] <- -90 - 180 * beta * sign(beta - 1)

-      # Update the start and end angles of the childs segment.

-      df[child, "start"] <- start

-      df[child, "end"] <- start + alpha

-      start <- start + alpha

     }

-  }

-

-  return(df)

+    return(df)

 }

@@ -303,7 +303,7 @@ layoutDaylight <- function( tree, branch.length ){

   i <- 1

   ave_change <- 1.0

   while( i <= MAX_COUNT & ave_change > MINIMUM_AVERAGE_ANGLE_CHANGE ){

-    cat('Iteration: ', i, '\n')

+      ## cat('Iteration: ', i, '\n')

     # Reset max_change after iterating over tree.

     total_max <- 0.0

@@ -320,7 +320,7 @@ layoutDaylight <- function( tree, branch.length ){

     ave_change <- total_max / length(nodes)

-    cat('Average angle change', ave_change,'\n')

+    ## cat('Average angle change', ave_change,'\n')

     i <- i + 1

   }

@@ -12,6 +12,7 @@ html_preview: false

 ```{r echo=FALSE, results="hide", message=FALSE}

 library("txtplot")

+library("badger")

 library("ypages")

 ```

@@ -36,7 +37,6 @@ library("ypages")

 [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/)

 [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree)

 [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

-[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -44,6 +44,15 @@ The `ggtree` package extending the `ggplot2` package. It based on grammar of gra

 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)

+

+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

+

++ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

++ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

++ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

++ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

+

+

 -----------------------------------------------------

 Please cite the following article when using `ggtree`:

@@ -52,21 +61,15 @@ __G Yu__, DK Smith, H Zhu, Y Guan, TTY Lam^\*^. ggtree: an R package for visuali

 `r badge_doi("10.1111/2041-210X.12628", "green")`

-`r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

 `r badge_altmetric("10533079", "green")`

 ----------------------------------------------------------------------------------------

-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

-

-+ [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

-+ [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

-+ [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

-+ [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

 ### Citation

 `r badge_citation("HtEfBTGE9r8C", "7268358477862164627", "green")`

+`r badge_sci_citation("http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004", "green")`

 ```{r echo=F, comment=NA}

@@ -4,56 +4,56 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-13972/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-14336/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

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+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--20-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

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+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree)

 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

 [![Twitter](https://img.shields.io/twitter/url/https/github.com/GuangchuangYu/ggtree.svg?style=social)](https://twitter.com/intent/tweet?hashtags=ggtree&url=http://onlinelibrary.wiley.com/doi/10.1111/2041-210X.12628/abstract&screen_name=guangchuangyu)

+For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

+

+-   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

+-   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

+-   [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

+-   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

+

 ------------------------------------------------------------------------

 Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.

-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-14-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![](https://img.shields.io/badge/Altmetric-348-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

 ------------------------------------------------------------------------

-For details, please visit our project website, <https://guangchuangyu.github.io/ggtree>.

-

--   [Documentation](https://guangchuangyu.github.io/ggtree/documentation/)

--   [FAQ](https://guangchuangyu.github.io/ggtree/faq/)

--   [Featured Articles](https://guangchuangyu.github.io/ggtree/featuredArticles/)

--   [Feedback](https://guangchuangyu.github.io/ggtree/#feedback)

-

 ### Citation

-[![citation](https://img.shields.io/badge/cited%20by-14-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+[![citation](https://img.shields.io/badge/cited%20by-15-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/cited%20in%20Web%20of%20Science%20Core%20Collection-6-green.svg?style=flat)](http://apps.webofknowledge.com/InboundService.do?mode=FullRecord&customersID=RID&IsProductCode=Yes&product=WOS&Init=Yes&Func=Frame&DestFail=http%3A%2F%2Fwww.webofknowledge.com&action=retrieve&SrcApp=RID&SrcAuth=RID&SID=U2EMQLA1958R5PUSAKt&UT=WOS%3A000393305300004)

        +-+---------+---------+---------+---------+---------+---+

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        +-+---------+---------+---------+---------+---------+---+

        2016     2016.2    2016.4    2016.6    2016.8     2017   

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-13972/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-14336/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

          ++-------------------+------------------+-------------------+------------------+--------------+

     3000 +                                                                                        *    +

@@ -12,7 +12,7 @@ geom_tree(mapping = NULL, data = NULL, layout = "rectangular",

 \item{data}{data}

-\item{layout}{one of 'rectangular', 'slanted', 'circular', 'radial' or 'unrooted'}

+\item{layout}{one of 'rectangular', 'slanted', 'circular', 'radial', 'equal_angle' or 'daylight'}

 \item{multiPhylo}{logical}

@@ -8,9 +8,8 @@

 \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",

-  layout.method = "equal_angle", open.angle = 0, mrsd = NULL,

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

+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",

   ndigits = NULL, ...)

 }

@@ -19,9 +18,7 @@ ggtree(tr, mapping = NULL, layout = "rectangular",

 \item{mapping}{aes mapping}

-\item{layout}{one of 'rectangular', 'slanted', 'fan', 'circular', 'radial' or 'unrooted'}

-

-\item{layout.method}{of 'equal_angle', 'daylight'.}

+\item{layout}{one of 'rectangular', 'slanted', 'fan', 'circular', 'radial', 'equal_angle' or 'daylight'}

 \item{open.angle}{open angle, only for 'fan' layout}