@@ -13,17 +13,19 @@ Description: 'ggtree' extends the 'ggplot2' plotting system which implemented

     the grammar of graphics. 'ggtree' is designed for visualization and annotation

     of phylogenetic trees with their covariates and other associated data.

 Depends:

-    R (>= 3.3.2),

+    R (>= 3.4.0),

     ggplot2 (>= 2.2.0),

-    treeio

+    treeio (>= 1.3.2)

 Imports:

     ape,

+    dplyr,

     grDevices,

     grid,

     magrittr,

     methods,

     rvcheck,

     scales,

+    tibble,

     tidyr,

     utils

 Suggests:

@@ -43,4 +45,4 @@ 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: 6.0.1.9000

+RoxygenNote: 6.0.1

@@ -2,8 +2,7 @@

 S3method(as.binary,phylo)

 S3method(as.data.frame,phylo)

-S3method(as.data.frame,treedata)

-S3method(fortify,beast)

+S3method(as_data_frame,treedata)

 S3method(fortify,codeml)

 S3method(fortify,codeml_mlc)

 S3method(fortify,hyphy)

@@ -81,6 +80,7 @@ export(nodeid)

 export(nodepie)

 export(open_tree)

 export(phylopic)

+export(range_format)

 export(reroot)

 export(rescale_tree)

 export(revts)

@@ -112,6 +112,7 @@ importFrom(ape,ladderize)

 importFrom(ape,read.tree)

 importFrom(ape,reorder.phylo)

 importFrom(ape,write.tree)

+importFrom(dplyr,full_join)

 importFrom(ggplot2,Geom)

 importFrom(ggplot2,GeomCurve)

 importFrom(ggplot2,GeomLabel)

@@ -190,6 +191,8 @@ importFrom(methods,setGeneric)

 importFrom(methods,setOldClass)

 importFrom(rvcheck,get_fun_from_pkg)

 importFrom(scales,alpha)

+importFrom(tibble,as_data_frame)

+importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

 importFrom(treeio,as.phylo)

 importFrom(treeio,as.treedata)

@@ -1,5 +1,6 @@

 CHANGES IN VERSION 1.11.2

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

+ o remove beast object support as read.beast output treedata object in treeio <2017-12-05, Tue>

  o deprecate subview, annotation_image and phylopic; remove theme_transparent <2017-12-04, Mon>

  o geom_tiplab now supports geom = "image" or geom = "phylopic" <2017-12-04, Mon>

  o A new layer geom_nodelab that equivalent to geom_tiplab but works for internal node <2017-12-04, Mon>

@@ -14,13 +14,14 @@ scaleX_by_time_from_mrsd <- function(df, mrsd, as.Date) {

     date <- Date2decimal(mrsd)

     df$x <- df$x + date - max(df$x)

-    df$branch <- (df[df$parent, "x"] + df[, "x"])/2

+    df$branch <- with(df, (x[match(parent, node)] + x)/2)

+    ## df$branch <- (df[df$parent, "x"] + df[, "x"])/2

     if (as.Date) {

         df$x <- decimal2Date(df$x)

         df$branch <- decimal2Date(df$branch)

     }

-    

+

     return(df)

 }

@@ -28,7 +29,7 @@ scaleX_by_time_from_mrsd <- function(df, mrsd, as.Date) {

 ##' convert Date to decimal format, eg "2014-05-05" to "2014.34"

 ##'

-##' 

+##'

 ##' @title Date2decimal

 ##' @param x Date

 ##' @return numeric

@@ -38,7 +39,7 @@ Date2decimal <- function(x) {

     if (is(x, "numeric")) {

         return(x)

     }

-    

+

     if (is(x, "character")) {

         x <- as.Date(x)

     }

@@ -49,7 +50,7 @@ Date2decimal <- function(x) {

 ##' convert decimal format to Date, eg "2014.34" to "2014-05-05"

 ##'

-##' 

+##'

 ##' @title decimal2Date

 ##' @param x numerical number, eg 2014.34

 ##' @return Date

@@ -1,31 +1,3 @@

-

-## ##' @export

-## ape::read.tree

-

-

-## ##' generate random tree

-## ##' @export

-## ##' @rdname rtree

-## ##' @param n number of tips in the tree

-## ##' @param rooted logcial

-## ##' @param tip.label tip label

-## ##' @param br one of the following: (i) an R function used to generate the

-## ##'           branch lengths ('rtree'; use 'NULL' to simulate only a

-## ##'           topology), or the coalescence times ('rcoal'); (ii) a

-## ##'           character to simulate a genuine coalescent tree for 'rcoal'

-## ##'           (the default); or (iii) a numeric vector for the branch

-## ##'           lengths or the coalescence times.

-## ##' @param ... additional parameters to be passed to 'br'

-## ##' @source

-## ##' This is just the imported function

-## ##' from the ape package. The documentation you should

-## ##' read for the rtree function can be found here: \link[ape]{rtree}

-## ##'

-## ##' @seealso

-## ##' \link[ape]{rtree}

-## rtree <- ape::rtree

-

-

 ##' merge phylo and output of boot.phylo to 'apeBootstrap' object

 ##'

 ##'

@@ -41,49 +13,3 @@ apeBoot <- function(phylo, boot) {

     as.treedata(phylo, boot)

 }

-## apeBoot <- function(phylo, boot) {

-##     ## phylo is a phylo object

-##     ## boot is output from boot.phylo

-##     new("apeBootstrap",

-##         phylo=phylo,

-##         bootstrap=data.frame(node=(1:Nnode(phylo)) + Ntip(phylo), bootstrap=boot)

-##         )

-## }

-

-

-## ##' @rdname show-methods

-## ##' @importFrom ape print.phylo

-## ##' @exportMethod show

-## setMethod("show", signature(object = "apeBootstrap"),

-##           function(object) {

-##               cat("'apeBoot' S4 object that stored bootstrap value generated by 'ape::boot.phylo'", ".\n\n")

-##               cat("...@ tree: ")

-##               print.phylo(get.tree(object))

-##           })

-

-

-

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

-## setMethod("groupClade", signature(object="apeBootstrap"),

-##           function(object, node, group_name="group") {

-##               groupClade_(object, node, group_name)

-##           })

-

-## ##' @rdname scale_color-methods

-## ##' @exportMethod scale_color

-## setMethod("scale_color", signature(object="apeBootstrap"),

-##           function(object, by="bootstrap", ...) {

-##               scale_color_(object, by, ...)

-##           })

-

-

-## ##' @rdname get.fields-methods

-## ##' @exportMethod get.fields

-## setMethod("get.fields", signature(object="apeBootstrap"),

-##           function(object, ...) {

-##               get.fields.tree(object)

-##           }

-##           )

-

new file mode 100644

@@ -0,0 +1,20 @@

+##' format a list of range (HPD, CI, etc that has length of 2)

+##'

+##'

+##' @title range_format

+##' @param x input list

+##' @param trans transformation function

+##' @return character vector of '[lower, upper]'

+##' @export

+##' @author guangchuang yu

+range_format <- function(x, trans = NULL) {

+    sapply(x, function(y) {

+        if(length(y) == 1 && is.na(y)) {

+            return(NA)

+        } else {

+            if (!is.null(trans) && is(trans, 'function'))

+                y <- trans(y)

+            return(sprintf("[%f, %f]", y[1], y[2]))

+        }

+    })

+}

@@ -3,12 +3,13 @@

 ##'

 ##' @title geom_range

 ##' @param range range, e.g. "height_0.95_HPD"

+##' @param branch.length corresponding branch.length

 ##' @param ... additional parameter, e.g. color, size, alpha

 ##' @return ggplot layer

 ##' @importFrom ggplot2 aes_string

 ##' @export

 ##' @author Guangchuang Yu

-geom_range <- function(range="height_0.95_HPD", ...) {

+geom_range <- function(range = "length_0.95_HPD", branch.length = "branch.length", ...) {

     position = "identity"

     show.legend = NA

     na.rm = TRUE

@@ -16,11 +17,10 @@ geom_range <- function(range="height_0.95_HPD", ...) {

     default_aes <- aes_(x=~x, y=~y, xend=~x, yend=~y)

-    if (grepl("^height", range)) {

-        mapping <- modifyList(default_aes, aes_string(branch.length="height", label=range))

-    } else {

-        mapping <- modifyList(default_aes, aes_string(branch.length="branch.length", label=range))

-    }

+    lower <- paste0('range_lower(', range, ')')

+    upper <- paste0('range_upper(', range, ')')

+

+    mapping <- modifyList(default_aes, aes_string(branch.length=branch.length, lower=lower, upper=upper))

     layer(

         stat = StatRange,

@@ -39,21 +39,28 @@ geom_range <- function(range="height_0.95_HPD", ...) {

 StatRange <- ggproto("StatRange", Stat,

                      compute_group = function(self, data, scales, params) {

-                         ## label is actually the range

-

-                         df <- data[!is.na(data[,"label"]),]

-                         rr <- gsub("\\[", "", df[,"label"])

-                         rr <- gsub("\\]", "", rr)

-                         rr2 <- strsplit(rr, split=',') %>% do.call('rbind', .)

-                         rr2 <- matrix(as.numeric(rr2), ncol=2, byrow=FALSE)

-                         rr2 <- rr2 + df$x - df$branch

-

-                         data.frame(x = rr2[,1],

-                                    xend = rr2[,2],

-                                    y = df$y,

-                                    yend = df$y)

+                         df <- data[!is.na(data[["lower"]]),]

+                         df[["lower"]] <- df[["lower"]] + df[["x"]] - df[["branch.length"]]

+                         df[["upper"]] <- df[["upper"]] + df[["x"]] - df[["branch.length"]]

+

+                         data.frame(x = df[["lower"]],

+                                    xend = df[["upper"]],

+                                    y = df[["y"]],

+                                    yend = df[["y"]])

                      },

                      required_aes = c("x", "y", "xend", "yend")

                      )

+range_lower <- function(range) {

+    sapply(range, function(x) as.numeric(x[1]))

+}

+

+range_upper <- function(range) {

+    sapply(range, function(x) {

+        if (length(x) == 1 && is.na(x))

+            return(NA)

+        as.numeric(x[2])

+    })

+}

+

@@ -106,118 +106,118 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

     invisible(tree)

 }

-##' @method fortify beast

-##' @export

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

-                          layout        = "rectangular",

-                          yscale        = "none",

-                          ladderize     = TRUE,

-                          right         = FALSE,

-                          branch.length = "branch.length",

-                          ndigits       = NULL,

-                          mrsd = NULL, ...) {

-

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

-    phylo <- model@phylo

-    df    <- fortify(phylo,

-                     layout = layout,

-                     branch.length = branch.length,

-                     ladderize = ladderize,

-                     right = right,

-                     mrsd = mrsd, ...)

-

-    stats <- model@stats

-

-    scn <- colnames(stats)

-    scn <- scn[scn != 'node']

-

-    for (cn in scn) {

-        if (cn %in% colnames(df)) {

-            colnames(stats)[colnames(stats) == cn] <- paste0(cn, "_")

-            msg <- paste("feature", cn, "was renamed to", paste0(cn, "_"), "due to name conflict...")

-            warning(msg)

-        }

-    }

-

-    idx <- which(colnames(stats) != "node")

-    for (ii in idx) {

-        if (is.character_beast(stats, ii)) {

-            len <- sapply(stats[,ii], length)

-            if (any(len > 1)) {

-                stats[,ii] %<>% sapply(., function(x) {

-                    y <- unlist(x) %>% as.character %>%

-                        gsub("\"", "", .) %>% gsub("'", "", .)

-                    if (length(y) == 1) {

-                        return(y)

-                    } else {

-                        return(paste0('{', paste0(y, collapse = ','), '}'))

-                    }

-                })

-            } else {

-                stats[,ii] %<>% unlist %>% as.character %>%

-                    gsub("\"", "", .) %>% gsub("'", "", .)

-            }

-            next

-        }

-

-        len <- sapply(stats[,ii], length)

-        if ( all(len == 1) ) {

-            stats[, ii] %<>% unlist %>% as.character %>% as.numeric

-            if (!is.null(ndigits)) {

-                stats[, ii] %<>% round(., ndigits)

-            }

-        } else if (all(len <= 2)) {

-            stats[, ii] %<>% sapply(., function(x) {

-                y <- unlist(x) %>% as.character %>% as.numeric

-                if (!is.null(ndigits)) {

-                    y %<>% round(., ndigits)

-                }

-                if (length(y) == 1) {

-                    return(y)

-                } else {

-                    return(paste0('[', paste0(y, collapse = ','), ']'))

-                }

-            })

-        } else {

-            stats[,ii] %<>% sapply(., function(x) {

-                y <- unlist(x) %>% as.character %>% as.numeric

-                if (!is.null(ndigits)) {

-                    y %<>% round(., ndigits)

-                }

-                if (length(y) == 1) {

-                    return(y)

-                } else {

-                    return(paste0('{', paste0(y, collapse = ','), '}'))

-                }

-            })

-        }

-    }

-

-

-    cn <- colnames(stats)

-    lo <- cn[grep("_lower", cn)]

-    hi <- gsub("lower$", "upper", lo)

-    rid <- gsub("_lower$", "", lo)

-

-    for (i in seq_along(rid)) {

-        stats[, rid[i]] <- paste0("[", stats[, lo[i]], ",", stats[, hi[i]], "]")

-        stats[is.na(stats[, lo[i]]), rid[i]] <- NA

-    }

-

-    idx   <- match(df$node, stats$node)

-    stats <- stats[idx,]

-    cn_stats <- colnames(stats)

-    stats <- stats[, cn_stats != "node"]

-

-    df <- cbind(df, stats)

-    if (is(stats, "data.frame") == FALSE) {

-        colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]

-    }

-

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

+## ##' @method fortify beast

+## ##' @export

+## fortify.beast <- function(model, data,

+##                           layout        = "rectangular",

+##                           yscale        = "none",

+##                           ladderize     = TRUE,

+##                           right         = FALSE,

+##                           branch.length = "branch.length",

+##                           ndigits       = NULL,

+##                           mrsd = NULL, ...) {

+

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

+##     phylo <- model@phylo

+##     df    <- fortify(phylo,

+##                      layout = layout,

+##                      branch.length = branch.length,

+##                      ladderize = ladderize,

+##                      right = right,

+##                      mrsd = mrsd, ...)

+

+##     stats <- model@stats

+

+##     scn <- colnames(stats)

+##     scn <- scn[scn != 'node']

+

+##     for (cn in scn) {

+##         if (cn %in% colnames(df)) {

+##             colnames(stats)[colnames(stats) == cn] <- paste0(cn, "_")

+##             msg <- paste("feature", cn, "was renamed to", paste0(cn, "_"), "due to name conflict...")

+##             warning(msg)

+##         }

+##     }

+

+##     idx <- which(colnames(stats) != "node")

+##     for (ii in idx) {

+##         if (is.character_beast(stats, ii)) {

+##             len <- sapply(stats[,ii], length)

+##             if (any(len > 1)) {

+##                 stats[,ii] %<>% sapply(., function(x) {

+##                     y <- unlist(x) %>% as.character %>%

+##                         gsub("\"", "", .) %>% gsub("'", "", .)

+##                     if (length(y) == 1) {

+##                         return(y)

+##                     } else {

+##                         return(paste0('{', paste0(y, collapse = ','), '}'))

+##                     }

+##                 })

+##             } else {

+##                 stats[,ii] %<>% unlist %>% as.character %>%

+##                     gsub("\"", "", .) %>% gsub("'", "", .)

+##             }

+##             next

+##         }

+

+##         len <- sapply(stats[,ii], length)

+##         if ( all(len == 1) ) {

+##             stats[, ii] %<>% unlist %>% as.character %>% as.numeric

+##             if (!is.null(ndigits)) {

+##                 stats[, ii] %<>% round(., ndigits)

+##             }

+##         } else if (all(len <= 2)) {

+##             stats[, ii] %<>% sapply(., function(x) {

+##                 y <- unlist(x) %>% as.character %>% as.numeric

+##                 if (!is.null(ndigits)) {

+##                     y %<>% round(., ndigits)

+##                 }

+##                 if (length(y) == 1) {

+##                     return(y)

+##                 } else {

+##                     return(paste0('[', paste0(y, collapse = ','), ']'))

+##                 }

+##             })

+##         } else {

+##             stats[,ii] %<>% sapply(., function(x) {

+##                 y <- unlist(x) %>% as.character %>% as.numeric

+##                 if (!is.null(ndigits)) {

+##                     y %<>% round(., ndigits)

+##                 }

+##                 if (length(y) == 1) {

+##                     return(y)

+##                 } else {

+##                     return(paste0('{', paste0(y, collapse = ','), '}'))

+##                 }

+##             })

+##         }

+##     }

+

+

+##     cn <- colnames(stats)

+##     lo <- cn[grep("_lower", cn)]

+##     hi <- gsub("lower$", "upper", lo)

+##     rid <- gsub("_lower$", "", lo)

+

+##     for (i in seq_along(rid)) {

+##         stats[, rid[i]] <- paste0("[", stats[, lo[i]], ",", stats[, hi[i]], "]")

+##         stats[is.na(stats[, lo[i]]), rid[i]] <- NA

+##     }

+

+##     idx   <- match(df$node, stats$node)

+##     stats <- stats[idx,]

+##     cn_stats <- colnames(stats)

+##     stats <- stats[, cn_stats != "node"]

+

+##     df <- cbind(df, stats)

+##     if (is(stats, "data.frame") == FALSE) {

+##         colnames(df)[colnames(df) == "stats"] <- cn_stats[cn_stats != "node"]

+##     }

+

+##     df <- scaleY(phylo, df, yscale, layout, ...)

-    append_extraInfo(df, model)

-}

+##     append_extraInfo(df, model)

+## }

 ##' @method fortify codeml

@@ -392,7 +392,7 @@ scaleY <- function(phylo, df, yscale, layout, ...) {

         warning("yscale is not available...\n")

         return(df)

     }

-    if (is.numeric(df[, yscale])) {

+    if (is.numeric(df[[yscale]])) {

         y <- getYcoord_scale_numeric(phylo, df, yscale, ...)

         ## if (order.y) {

         ##     y <- getYcoord_scale2(phylo, df, yscale)

@@ -68,15 +68,15 @@ setMethod("gzoom", signature(object="ggtree"),

 ##           })

-##' zoom selected subtree

-##'

-##'

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

-setMethod("gzoom", signature(object="beast"),

-          function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

-              gzoom.phylo(get.tree(object), focus, subtree, widths)

-          })

+## ##' zoom selected subtree

+## ##'

+## ##'

+## ##' @rdname gzoom-methods

+## ##' @exportMethod gzoom

+## setMethod("gzoom", signature(object="beast"),

+##           function(object, focus, subtree=FALSE, widths=c(.3, .7)) {

+##               gzoom.phylo(get.tree(object), focus, subtree, widths)

+##           })

 ##' @rdname gzoom-methods

 ##' @exportMethod gzoom

@@ -85,7 +85,9 @@ setMethod("gzoom", signature(object="codeml"),

               gzoom.phylo(get.tree(object), focus, subtree, widths)

           })

-

+##' zoom selected subtree

+##'

+##'

 ##' @rdname gzoom-methods

 ##' @exportMethod gzoom

 setMethod("gzoom", signature(object="treedata"),

@@ -1,16 +1,16 @@

-##' @rdname reroot-methods

-##' @exportMethod reroot

-setMethod("reroot", signature(object="beast"),

-          function(object, node, ...) {

-              object@phylo <- reroot(object@phylo, node, ...)

+## ##' @rdname reroot-methods

+## ##' @exportMethod reroot

+## setMethod("reroot", signature(object="beast"),

+##           function(object, node, ...) {

+##               object@phylo <- reroot(object@phylo, node, ...)

-              node_map <- attr(object@phylo, "node_map")

-              idx <- match(object@stats$node, node_map[,1])

-              object@stats$node <- node_map[idx, 2]

+##               node_map <- attr(object@phylo, "node_map")

+##               idx <- match(object@stats$node, node_map[,1])

+##               object@stats$node <- node_map[idx, 2]

-              return(object)

-          })

+##               return(object)

+##           })

 ## ##' @rdname reroot-methods

 ## ##' @exportMethod reroot

@@ -1,14 +1,16 @@

+## ##' scale color by a numerical tree attribute

+## ##'

+## ##'

+## ##' @rdname scale_color-methods

+## ##' @exportMethod scale_color

+## setMethod("scale_color", signature(object="beast"),

+##           function(object, by, ...) {

+##               scale_color_(object, by, ...)

+##           })

+

 ##' scale color by a numerical tree attribute

 ##'

 ##'

-##' @rdname scale_color-methods

-##' @exportMethod scale_color

-setMethod("scale_color", signature(object="beast"),

-          function(object, by, ...) {

-              scale_color_(object, by, ...)

-          })

-

-

 ##' @rdname scale_color-methods

 ##' @exportMethod scale_color

 setMethod("scale_color", signature(object="treedata"),

@@ -18,14 +18,12 @@ fortify.treedata <- function(model, data, layout="rectangular", yscale="none",

     }

     ypos <- getYcoord(x)

     N <- Nnode(x, internal.only=FALSE)

-    xypos <- data.frame(node=1:N, x=xpos, y=ypos)

+    xypos <- data_frame(node=1:N, x=xpos, y=ypos)

-    df <- as.data.frame(model, branch.length="branch.length") # already set by set_branch_length

-    idx <- is.na(df$parent)

-    df$parent[idx] <- df$node[idx]

-    rownames(df) <- df$node

+    df <- as_data_frame(model, branch.length="branch.length") # already set by set_branch_length

+    ##rownames(df) <- as.character(df$node)

-    res <- merge(df, xypos, by='node', all.y=TRUE)

+    res <- full_join(df, xypos, by = "node")

     ## add branch mid position

     res <- calculate_branch_mid(res)

@@ -39,31 +37,41 @@ fortify.treedata <- function(model, data, layout="rectangular", yscale="none",

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

 }

-##' @method as.data.frame treedata

+##' @method as_data_frame treedata

+##' @importFrom tibble as_data_frame

 ##' @export

 ## @importFrom treeio Nnode

 ## @importFrom treeio Ntip

-as.data.frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {

+as_data_frame.treedata <- function(x, row.names, optional, branch.length = "branch.length", ...) {

     tree <- set_branch_length(x, branch.length)

     ## res <- as.data.frame(tree@phylo)

-    res <- as.data.frame_(tree@phylo)

-    tree_anno <- get_tree_data(x)

+    res <- as_data_frame_(tree@phylo)

+    tree_anno <- as_data_frame(get_tree_data(x))

     if (nrow(tree_anno) > 0) {

-        res <- merge(res, tree_anno, by="node", all.x=TRUE)

+        by <- "node"

+        tree_anno$node <- as.integer(tree_anno$node)

+        if ("parent" %in% colnames(tree_anno)) {

+            by <- c(by, "parent")

+            tree_anno$parent <- as.integer(tree_anno$parent)

+        }

+

+        res <- full_join(res, tree_anno, by=by)

     }

     return(res)

 }

 ##@method as.data.frame phylo

 ##@export

-as.data.frame_ <- function(x, row.names, optional, branch.length = "branch.length", ...) {

+##' @importFrom tibble data_frame

+##' @importFrom dplyr full_join

+as_data_frame_ <- function(x, row.names, optional, branch.length = "branch.length", ...) {

     phylo <- x

     ntip <- Ntip(phylo)

     N <- Nnode(phylo, internal.only=FALSE)

     tip.label <- phylo[["tip.label"]]

-    res <- as.data.frame(phylo[["edge"]])

+    res <- as_data_frame(phylo[["edge"]])

     colnames(res) <- c("parent", "node")

     if (!is.null(phylo$edge.length))

         res$branch.length <- phylo$edge.length

@@ -73,11 +81,14 @@ as.data.frame_ <- function(x, row.names, optional, branch.length = "branch.lengt

     if ( !is.null(phylo$node.label) ) {

         label[(ntip+1):N] <- phylo$node.label

     }

-    label.df <- data.frame(node=1:N, label=label)

-    res <- merge(res, label.df, by='node', all.y=TRUE)

     isTip <- rep(FALSE, N)

     isTip[1:ntip] <- TRUE

-    res$isTip <- isTip

+

+    label.df <- data_frame(node=1:N, label=label, isTip = isTip)

+    res <- full_join(res, label.df, by='node')

+

+    idx <- is.na(res$parent)

+    res$parent[idx] <- res$node[idx]

     return(res)

 }

@@ -1449,7 +1460,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {

 }

 .assign_parent_status <- function(tr, df, variable) {

-    yy <- df[, variable]

+    yy <- df[[variable]]

     na.idx <- which(is.na(yy))

     if (length(na.idx) > 0) {

         tree <- get.tree(tr)

@@ -1470,7 +1481,7 @@ getYcoord_scale_numeric <- function(tr, df, yscale, ...) {

 }

 .assign_child_status <- function(tr, df, variable, yscale_mapping=NULL) {

-    yy <- df[, variable]

+    yy <- df[[variable]]

     if (!is.null(yscale_mapping)) {

         yy <- yscale_mapping[yy]

     }

@@ -1507,7 +1518,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {

     }

     if (yscale == "label") {

-        yy <- df[, yscale]

+        yy <- df[[yscale]]

         ii <- which(is.na(yy))

         if (length(ii)) {

             df[ii, yscale] <- df[ii, "node"]

@@ -1518,7 +1529,7 @@ getYcoord_scale_category <- function(tr, df, yscale, yscale_mapping=NULL, ...) {

     df <- .assign_parent_status(tr, df, yscale)

     df <- .assign_child_status(tr, df, yscale, yscale_mapping)

-    y <- df[, yscale]

+    y <- df[[yscale]]

     if (anyNA(y)) {

         warning("NA found in y scale mapping, all were setting to 0")

@@ -1543,7 +1554,8 @@ add_angle_slanted <- function(res) {

 }

 calculate_branch_mid <- function(res) {

-    res$branch <- (res[res$parent, "x"] + res[, "x"])/2

+    res$branch <- with(res, (x[match(parent, node)] + x)/2)

+    ## res$branch <- (res[match(res$parent, res$node), "x"] + res[, "x"])/2

     if (!is.null(res$length)) {

         res$length[is.na(res$length)] <- 0

     }

@@ -1566,6 +1578,9 @@ set_branch_length <- function(tree_object, branch.length) {

     tree_anno <- get_tree_data(tree_object)

+    if (is(tree_anno, "matrix"))

+        tree_anno <- as.data.frame(tree_anno)

+

     phylo <- get.tree(tree_object)

     cn <- colnames(tree_anno)

@@ -1573,7 +1588,7 @@ set_branch_length <- function(tree_object, branch.length) {

     length <- match.arg(branch.length, cn)

-    if (all(is.na(as.numeric(tree_anno[, length])))) {

+    if (all(is.na(as.numeric(tree_anno[[length]])))) {

         stop("branch.length should be numerical attributes...")

     }

@@ -1584,7 +1599,7 @@ set_branch_length <- function(tree_object, branch.length) {

                 by  = "node",

                 all.x = TRUE)

     dd <- dd[match(edge$node, dd$node),]

-    len <- unlist(dd[, length])

+    len <- unlist(dd[[length]])

     len <- as.numeric(len)

     len[is.na(len)] <- 0

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

 ---

 output:

   md_document:

-    variant: gfm

+    variant: markdown_github

 html_preview: false

 ---

@@ -1,70 +1,35 @@

 <!-- README.md is generated from README.Rmd. Please edit that file -->

-

-# ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

+ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data

+===========================================================================================================================

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

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree)

-[![develVersion](https://img.shields.io/badge/devel%20version-1.11.1-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)

-[![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-

-[![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--12--04-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)

-

-[![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)

-[![Backers on Open

-Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers)

-[![Sponsors on Open

-Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

-

-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.

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.10.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.11.2-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) [![total](https://img.shields.io/badge/downloads-21911/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1156/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+

+[![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--12--05-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)

+

+[![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) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

+

+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>.

+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)

+-   [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.

+**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.

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)

-[![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

-[![citation](https://img.shields.io/badge/cited%20by-51-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-333-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-52-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

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