@@ -9,6 +9,8 @@ S3method(fortify,phylo4)

 S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

 S3method(fortify,treedata)

+S3method(groupClade,ggtree)

+S3method(groupOTU,ggtree)

 S3method(identify,gg)

 S3method(print,beastList)

 export("%+>%")

@@ -90,8 +92,6 @@ export(theme_tree2)

 export(viewClade)

 export(xlim_expand)

 export(xlim_tree)

-exportMethods(groupClade)

-exportMethods(groupOTU)

 exportMethods(gzoom)

 exportMethods(reroot)

 exportMethods(scale_color)

@@ -185,13 +185,13 @@ importFrom(scales,alpha)

 importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

 importFrom(tidytree,as_data_frame)

+importFrom(tidytree,get_tree_data)

+importFrom(tidytree,groupClade)

+importFrom(tidytree,groupOTU)

 importFrom(treeio,Nnode)

 importFrom(treeio,Ntip)

 importFrom(treeio,as.phylo)

 importFrom(treeio,as.treedata)

-importFrom(treeio,get_tree_data)

-importFrom(treeio,groupClade)

-importFrom(treeio,groupOTU)

 importFrom(utils,modifyList)

 importFrom(utils,packageDescription)

 importFrom(utils,packageVersion)

@@ -7,20 +7,6 @@ as.binary <- function(tree, ...) {

     UseMethod("as.binary")

 }

-## ##' plot method generics

-## ##'

-## ##'

-## ##' @docType methods

-## ##' @name plot

-## ##' @rdname plot-methods

-## ##' @title plot method

-## ##' @param x object

-## ##' @param ... Additional argument list

-## ##' @return plot

-## ##' @importFrom stats4 plot

-## ##' @export

-## if ( !isGeneric("plot") )

-## 	setGeneric("plot", function(x, ...) standardGeneric("plot"))

 ##' @docType methods

 ##' @name reroot

@@ -34,112 +20,6 @@ as.binary <- function(tree, ...) {

 ##' @export

 setGeneric("reroot", function(object, node, ...) standardGeneric("reroot"))

-## ##' @docType methods

-## ##' @name get.tree

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

-## ##' @title get.tree method

-## ##' @param object one of \code{phylo}, \code{jplace}, \code{nhx}, \code{phangorn}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object

-## ##' @param ... additional parameter

-## ##' @return phylo object

-## ##' @export

-## setGeneric("get.tree", function(object, ...) standardGeneric("get.tree"))

-

-## ##' @docType methods

-## ##' @name get.treetext

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

-## ##' @title get.treetext method

-## ##' @param object one of \code{phylo}, \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object

-## ##' @param ... additional parameter

-## ##' @return phylo object

-## ##' @export

-## setGeneric("get.treetext", function(object, ...) standardGeneric("get.treetext"))

-

-

-## ##' @docType methods

-## ##' @name get.treeinfo

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

-## ##' @title get.treeinfo method

-## ##' @param object jplace object

-## ##' @param layout layout

-## ##' @param ladderize ladderize, logical

-## ##' @param right logical, parameter for ladderize

-## ##' @param ... additional parameter

-## ##' @return data.frame

-## ##' @export

-## setGeneric("get.treeinfo", function(object, layout="phylogram", ladderize=TRUE, right=FALSE, ...) standardGeneric("get.treeinfo"))

-

-

-## ##' @docType methods

-## ##' @name get.fields

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

-## ##' @title get.fields method

-## ##' @param object one of \code{jplace}, \code{beast}, \code{hyphy}, \code{codeml}, \code{codeml_mlc}, \code{paml_rst} object

-## ##' @param ... additional parameter

-## ##' @return available annotation variables

-## ##' @export

-## setGeneric("get.fields", function(object, ...) standardGeneric("get.fields"))

-

-

-## ##' @docType methods

-## ##' @name get.placements

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

-## ##' @title get.placements method

-## ##' @param object jplace object

-## ##' @param by get best hit or others

-## ##' @param ... additional parameter

-## ##' @return data.frame

-## ##' @export

-## setGeneric("get.placements", function(object, by, ...) standardGeneric("get.placements"))

-

-## ##' @docType methods

-## ##' @name get.subs

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

-## ##' @title get.subs method

-## ##' @param object paml_rst object

-## ##' @param type one of 'marginal_subs', 'marginal_AA_subs',

-## ##'                     'joint_subs' or 'joint_AA_subs'.

-## ##' @param ... additional parameter

-## ##' @return data.frame

-## ##' @export

-## setGeneric("get.subs", function(object, type, ...) standardGeneric("get.subs"))

-

-

-## ##' @docType methods

-## ##' @name get.tipseq

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

-## ##' @title get.tipseq method

-## ##' @param object one of paml_rst or codeml object

-## ##' @param ... additional parameter

-## ##' @return character

-## ##' @export

-## setGeneric("get.tipseq", function(object, ...) standardGeneric("get.tipseq"))

-

-## ##' @docType methods

-## ##' @name groupOTU

-## ##' @rdname groupOTU-methods

-## ##' @title groupOTU method

-## ##' @param object supported objects, including phylo, paml_rst,

-## ##'               codeml_mlc, codeml, jplace, beast, hyphy

-## ##' @param focus a vector of tip (label or number) or a list of tips.

-## ##' @param group_name name of the group, 'group' by default

-## ##' @param ... additional parameter

-## ##' @return group index

-## ##' @export

-## setGeneric("groupOTU", function(object, focus, group_name="group", ...) standardGeneric("groupOTU"))

-

-## ##' @docType methods

-## ##' @name groupClade

-## ##' @rdname groupClade-methods

-## ##' @title groupClade method

-## ##' @param object supported objects, including phylo, paml_rst,

-## ##'               codeml_mlc, codeml, jplace, beast, hyphy

-## ##' @param node a internal node or a vector of internal nodes

-## ##' @param group_name name of the group, 'group' by default

-## ##' @param ... additional parameter

-## ##' @return group index

-## ##' @export

-## setGeneric("groupClade", function(object, node, group_name="group", ...) standardGeneric("groupClade"))

-

 ##' @docType methods

 ##' @name scale_color

@@ -166,18 +46,3 @@ setGeneric("scale_color", function(object, by, ...) standardGeneric("scale_color

 ##' @export

 setGeneric("gzoom", function(object, focus, subtree=FALSE, widths=c(.3, .7), ...) standardGeneric("gzoom"))

-

-## ##' @docType methods

-## ##' @name drop.tip

-## ##' @rdname drop.tip-methods

-## ##' @title drop.tip method

-## ##' @param object An nhx or phylo object

-## ##' @param tip a vector of mode numeric or character specifying the tips to delete

-## ##' @param ... additional parameters

-## ##' @return updated object

-## ##' @export

-## setGeneric (

-## 	name = "drop.tip",

-## 	def = function( object, tip, ... )

-## 		{ standardGeneric("drop.tip") }

-## )

@@ -82,7 +82,7 @@ fortify.phylo <- function(model, data,

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

 }

-##' @importFrom treeio get_tree_data

+##' @importFrom tidytree get_tree_data

 set_branch_length <- function(tree_object, branch.length) {

     if (branch.length == "branch.length") {

         return(tree_object)

deleted file mode 100644

@@ -1,70 +0,0 @@

-## ##' drop.tip method

-## ##'

-## ##'

-## ##' @rdname drop.tip-methods

-## ##' @aliases drop.tip,nhx

-## ##' @exportMethod drop.tip

-## ##' @author Casey Dunn \url{http://dunnlab.org}  and Guangchuang Yu \url{https://guangchuangyu.github.io}

-## ##' @usage drop.tip(object, tip, ...)

-## setMethod("drop.tip", signature(object="nhx"),

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

-

-##               ## label the internal tree nodes by their number

-##               no_node_label <- FALSE

-##               if (is.null(object@phylo$node.label)) {

-##                   object@phylo$node.label <- Ntip(object) + (1:Nnode(object))

-##                   no_node_label <- TRUE

-##               }

-

-##               ## Prepare the nhx object for subsampling

-##               object@nhx_tags$node <- as.numeric(object@nhx_tags$node)

-##               object@nhx_tags <- object@nhx_tags[order(object@nhx_tags$node),]

-

-##               ## add a colmn that has labels for both tips and internal nodes

-##               object@nhx_tags$node.label <- c(object@phylo$tip.label, as.character(object@phylo$node.label))

-

-##               ## Will need to take different approaches for subsampling tips

-##               ## and internal nodes, add a column to make it easy to tell them apart

-##               object@nhx_tags$is_tip <- object@nhx_tags$node <= Ntip(object)

-

-##               ## Remove tips

-##               object@phylo = ape::drop.tip( object@phylo, tip )

-

-##               ## Subsample the tags

-##               object@nhx_tags = object@nhx_tags[object@nhx_tags$node.label %in% (c(object@phylo$tip.label, as.character(object@phylo$node.label))),]

-

-##               ## Update tip node numbers

-##               tip_nodes <- object@nhx_tags$node.label[ object@nhx_tags$is_tip ]

-##               object@nhx_tags$node[ object@nhx_tags$is_tip ] = match(object@phylo$tip.label, tip_nodes)

-

-##               internal_nodes <- object@nhx_tags$node.label[ !object@nhx_tags$is_tip ]

-##               object@nhx_tags$node[ !object@nhx_tags$is_tip ] = match(object@phylo$node.label, internal_nodes) + length(object@phylo$tip.label)

-

-##               ## Clean up

-##               object@nhx_tags$node.label = NULL

-##               object@nhx_tags$is_tip = NULL

-##               if (no_node_label) {

-##                   object@phylo$node.label <- NULL

-##               }

-

-##               return(object)

-##           })

-

-

-

-

-

-## ##' @rdname drop.tip-methods

-## ##' @exportMethod drop.tip

-## ##' @aliases drop.tip,phylo

-## ##' @source

-## ##' drop.tip for phylo object is a wrapper method of ape::drop.tip

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

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

-## ##'

-## ##' @seealso

-## ##' \link[ape]{drop.tip}

-## setMethod("drop.tip", signature(object="phylo"),

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

-##               ape::drop.tip(object, tip, ...)

-##           })

@@ -618,6 +618,3 @@ fortify.phyloseq <- function(model, data,

 ## }

-

-

-has.extraInfo <- treeio:::has.extraInfo

@@ -1,109 +1,6 @@

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade_(object, node, group_name)

-##           })

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade_(object, node, group_name)

-##           }

-##           )

-

-##' groupClade method for ggtree object

-##'

-##'

-##' @name groupClade

-##' @title groupClade method

-##' @rdname groupClade-methods

-##' @param object ggtree object

-##' @param node internal node number

-##' @param group_name name of the group

-##' @importFrom treeio groupClade

-##' @exportMethod groupClade

-##' @aliases groupClade,ggtree-method

-setMethod("groupClade", signature(object="ggtree"),

-          function(object, node, group_name) {

-              groupClade.ggtree(object, node, group_name)

-          })

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade_(object, node, group_name)

-##           }

-##           )

-

-## ##' group selected clade

-## ##'

-## ##'

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade_(object, node, group_name)

-##           })

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade_(object, node, group_name)

-##           })

-

-

-## ##' @rdname groupClade-methods

-## ##' @exportMethod groupClade

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

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

-##               groupClade.phylo(object, node, group_name)

-##           })

-

-

-

-## groupClade.phylo <- function(object, node, group_name) {

-##     if (length(node) == 1) {

-##         clade <- extract.clade(object, node)

-##         tips <- clade$tip.label

-##     } else {

-##         tips <- lapply(node, function(x) {

-##             clade <- extract.clade(object, x)

-##             clade$tip.label

-##         })

-##     }

-

-##     groupOTU.phylo(object, tips, group_name)

-## }

-

-

-## groupClade_ <- function(object, node, group_name) {

-##     if (is(object, "phylo")) {

-##         object <- groupClade.phylo(object, node, group_name)

-##     } else {

-##         object@phylo <- groupClade.phylo(get.tree(object), node, group_name)

-##     }

-##     return(object)

-## }

-

-

-groupClade.ggtree <- function(object, nodes, group_name) {

-    df <- object$data

-    df[, group_name] <- 0

-    for (node in nodes) {

-        df <- groupClade.tbl(df, node, group_name)

-    }

-    df[, group_name] <- factor(df[[group_name]])

-    object$data <- df

-    return(object)

-}

-

-groupClade.tbl <- function(df, node, group_name) {

-    foc <- c(node, get.offspring.df(df, node))

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

-    df[idx, group_name] <- max(df[[group_name]]) + 1

-    return(df)

+##' @importFrom tidytree groupClade

+##' @method groupClade ggtree

+##' @export

+groupClade.ggtree <- function(.data, .node, group_name = "group", ...) {

+    .data$data <- groupClade(.data$data, .node, group_name, ...)

 }

@@ -1,251 +1,7 @@

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

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

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="beast"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="codeml"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="codeml_mlc"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="jplace"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="nhx"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="phangorn"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="phylip"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="paml_rst"),

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

-##               groupOTU_(object, focus, group_name, ...)

-##           }

-##           )

-

-

-## ##' group tree based on selected OTU, will traceback to MRCA

-## ##'

-## ##'

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## setMethod("groupOTU", signature(object="phylo"),

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

-##               groupOTU.phylo(object, focus, group_name, ...)

-##           })

-

-## ##' @rdname groupOTU-methods

-## ##' @exportMethod groupOTU

-## ##' @param tree which tree selected

-## setMethod("groupOTU", signature(object="r8s"),

-##           function(object, focus, group_name="group", tree="TREE", ...) {

-##               groupOTU_(get.tree(object)[[tree]], focus, group_name, ...)

-##           }

-##           )

-

-

-

-

-## ##' @importFrom ape which.edge

-## gfocus <- function(phy, focus, group_name, focus_label=NULL, overlap="overwrite") {

-##     overlap <- match.arg(overlap, c("origin", "overwrite", "abandon"))

-

-##     if (is.character(focus)) {

-##         focus <- which(phy$tip.label %in% focus)

-##     }

-

-##     n <- getNodeNum(phy)

-##     if (is.null(attr(phy, group_name))) {

-##         foc <- rep(0, n)

-##     } else {

-##         foc <- attr(phy, group_name)

-##     }

-##     i <- max(suppressWarnings(as.numeric(foc)), na.rm=TRUE) + 1

-##     if (is.null(focus_label)) {

-##         focus_label <- i

-##     }

-

-##     ## sn <- phy$edge[which.edge(phy, focus),] %>% as.vector %>% unique

-##     hit <- unique(as.vector(phy$edge[which.edge(phy, focus),]))

-##     if (overlap == "origin") {

-##         sn <- hit[is.na(foc[hit]) | foc[hit] == 0]

-##     } else if (overlap == "abandon") {

-##         idx <- !is.na(foc[hit]) & foc[hit] != 0

-##         foc[hit[idx]] <- NA

-##         sn <- hit[!idx]

-##     } else {

-##         sn <- hit

-##     }

-

-##     if (length(sn) > 0) {

-##         foc[sn] <- focus_label

-##     }

-

-##     attr(phy, group_name) <- foc

-##     phy

-## }

-

-

-## ##' group OTU

-## ##'

-## ##'

-## ##' @title groupOTU.phylo

-## ##' @param phy tree object

-## ##' @param focus tip list

-## ##' @param group_name name of the group

-## ##' @param ... additional parameters

-## ##' @return phylo object

-## ##' @author ygc

-## groupOTU.phylo <- function(phy, focus, group_name="group", ...) {

-##     attr(phy, group_name) <- NULL

-##     if ( is(focus, "list") ) {

-##         for (i in 1:length(focus)) {

-##             phy <- gfocus(phy, focus[[i]], group_name, names(focus)[i], ...)

-##         }

-##     } else {

-##         phy <- gfocus(phy, focus, group_name, ...)

-##     }

-##     res <- attr(phy, group_name)

-##     res[is.na(res)] <- 0

-##     attr(phy, group_name) <- factor(res)

-##     return(phy)

-## }

-

-## groupOTU_ <- function(object, focus, group_name, ...) {

-##     if (is(object, "phylo")) {

-##         object <- groupOTU.phylo(object, focus, group_name, ...)

-##     } else {

-##         object@phylo <- groupOTU.phylo(get.tree(object), focus, group_name, ...)

-##     }

-##     return(object)

-## }

-

-##' groupOTU method for ggtree object

-##'

-##'

-##' @name groupOTU

-##' @title groupOTU method

-##' @rdname groupOTU-methods

-##' @param object ggtree object

-##' @param focus OTU to focus

-##' @param group_name name of the group

-##' @param ... additional parameters

-##' @importFrom treeio groupOTU

-##' @exportMethod groupOTU

-##' @aliases groupOTU,ggtree-method

-setMethod("groupOTU", signature(object="ggtree"),

-          function(object, focus, group_name="group", ...) {

-              groupOTU.ggtree(object, focus, group_name, ...)

-          })

-

-

-groupOTU.ggtree <- function(object, focus, group_name, ...) {

-    df <- object$data

-    df[[group_name]] <- 0

-    object$data <- groupOTU.tbl(df, focus, group_name, ...)

-    return(object)

-}

-

-

-groupOTU.tbl <- function(df, focus, group_name, ...) {

-    if (is(focus, "list")) {

-        for (i in 1:length(focus)) {

-            df <- gfocus.tbl(df, focus[[i]], group_name, names(focus)[i], ...)

-        }

-    } else {

-        df <- gfocus.tbl(df, focus, group_name, ...)

-    }

-    df[[group_name]] <- factor(df[[group_name]])

-    return(df)

-}

-

-gfocus.tbl <- function(df, focus, group_name, focus_label=NULL, overlap="overwrite") {

-    overlap <- match.arg(overlap, c("origin", "overwrite", "abandon"))

-

-    focus <- df$node[which(df$label %in% focus)]

-    if (is.null(focus_label))

-        focus_label <- max(suppressWarnings(as.numeric(df[[group_name]])), na.rm=TRUE) + 1

-

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

-        hit <- match(focus, df$node)

-    } else {

-        anc <- getAncestor.df(df, focus[1])

-        foc <- c(focus[1], anc)

-        for (j in 2:length(focus)) {

-            anc2 <- getAncestor.df(df, focus[j])

-            comAnc <- intersect(anc, anc2)

-            foc <- c(foc, focus[j], anc2)

-            foc <- foc[! foc %in% comAnc]

-            foc <- c(foc, comAnc[1])

-        }

-        hit <- match(foc, df$node)

-    }

-

-    foc <- df[[group_name]]

-    if (overlap == "origin") {

-        sn <- hit[is.na(foc[hit]) | foc[hit] == 0]

-    } else if (overlap == "abandon") {

-        idx <- !is.na(foc[hit]) & foc[hit] != 0

-        foc[hit[idx]] <- NA

-        sn <- hit[!idx]

-    } else {

-        sn <- hit

-    }

-

-    if (length(sn) > 0) {

-        foc[sn] <- focus_label

-    }

-

-    df[, group_name] <- foc

-    return(df)

+##' @method groupOTU ggtree

+##' @export

+##' @importFrom tidytree groupOTU

+groupOTU.ggtree <- function(.data, .node, group_name = "group", ...) {

+    .data$data <- groupOTU(.data$data, .node, group_name, ...)

+    return(.data)

 }

@@ -1,30 +1,4 @@

-## ##' @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]

-

-##               return(object)

-##           })

-

-## ##' @rdname reroot-methods

-## ##' @exportMethod reroot

-## setMethod("reroot", signature(object="raxml"),

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

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

-

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

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

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

-

-##               return(object)

-##           })

-

 ##' reroot a tree

 ##'

@@ -1,8 +1,6 @@

 has.slot <- treeio:::has.slot

 getNodeNum <- treeio:::getNodeNum

-getRoot <- treeio:::getRoot

-has.field <- treeio:::has.field

-#append_extraInfo <- treeio:::append_extraInfo

+getRoot <- treeio:::rootnode

 get.tree <- treeio::get.tree

 drop.tip <- treeio::drop.tip

 get.fields <- treeio::get.fields

@@ -4,9 +4,9 @@ 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" />

-[![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-1.11.3-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-22066/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![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-1.11.3-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-22199/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/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--08-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)

+[![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--11-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)

@@ -27,7 +27,7 @@ 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.

-[![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-334-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)

+[![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-334-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-53-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

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

@@ -37,7 +37,7 @@ Please cite the following article when using `ggtree`:

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-22066/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/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) [![total](https://img.shields.io/badge/downloads-22199/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1218/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="docs/images/dlstats.png" width="890"/>

Binary files a/docs/images/citation.png and b/docs/images/citation.png differ

deleted file mode 100644

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

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/method-groupClade.R

-\docType{methods}

-\name{groupClade}

-\alias{groupClade}

-\alias{groupClade,ggtree-method}

-\title{groupClade method}

-\usage{

-\S4method{groupClade}{ggtree}(object, node, group_name)

-}

-\arguments{

-\item{object}{ggtree object}

-

-\item{node}{internal node number}

-

-\item{group_name}{name of the group}

-}

-\description{

-groupClade method for ggtree object

-}

deleted file mode 100644

@@ -1,22 +0,0 @@

-% Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/method-groupOTU.R

-\docType{methods}

-\name{groupOTU}

-\alias{groupOTU}

-\alias{groupOTU,ggtree-method}

-\title{groupOTU method}

-\usage{

-\S4method{groupOTU}{ggtree}(object, focus, group_name = "group", ...)

-}

-\arguments{

-\item{object}{ggtree object}

-

-\item{focus}{OTU to focus}

-

-\item{group_name}{name of the group}

-

-\item{...}{additional parameters}

-}

-\description{

-groupOTU method for ggtree object

-}

@@ -73,21 +73,21 @@ The `ggtree` package defined several functions to manipulate tree view. _`groupC

 Both _`groupClade`_ and _`groupOTU`_ work fine with tree and graphic object.

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-tree <- groupClade(tree, node=21)

+tree <- groupClade(tree, .node=21)

 ggtree(tree, aes(color=group, linetype=group))

 ```

 The following command will produce the same figure.

 ```{r eval=FALSE}

-ggtree(read.tree(nwk)) %>% groupClade(node=21) + aes(color=group, linetype=group)

+ggtree(read.tree(nwk)) %>% groupClade(.node=21) + aes(color=group, linetype=group)

 ```

 With `groupClade` and `groupOTU`, it's easy to highlight selected taxa and easy to select taxa to display related features.

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}

-tree <- groupClade(tree, node=c(21, 17))

+tree <- groupClade(tree, .node=c(21, 17))

 ggtree(tree, aes(color=group, linetype=group)) + geom_tiplab(aes(subset=(group==2)))

 ```

@@ -97,7 +97,7 @@ _`groupOTU`_ accepts a vector of OTUs (taxa name) or a list of OTUs.  _`groupOTU

 ```{r}

-tree <- groupOTU(tree, focus=c("D", "E", "F", "G"))

+tree <- groupOTU(tree, .node=c("D", "E", "F", "G"))

 ```

 ```{r fig.width=5, fig.height=5, fig.align="center", warning=FALSE}