@@ -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: 1.11.2

+Version: 1.11.3

 Authors@R: c(

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

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

@@ -36,6 +36,10 @@ check2: build

 	cd ..;\

 	R CMD check $(PKGNAME)_$(PKGVERS).tar.gz

+check3: rd build2

+	cd ..;\

+	R CMD check --ignore-vignettes $(PKGNAME)_$(PKGVERS).tar.gz

+

 bioccheck:

 	cd ..;\

 	Rscript -e 'BiocCheck::BiocCheck("$(PKGNAME)_$(PKGVERS).tar.gz")'

@@ -4,20 +4,12 @@ S3method(as.binary,phylo)

 S3method(as.data.frame,phylo)

 S3method(as_data_frame,phylo)

 S3method(as_data_frame,treedata)

-S3method(fortify,codeml)

-S3method(fortify,codeml_mlc)

-S3method(fortify,hyphy)

-S3method(fortify,jplace)

 S3method(fortify,multiPhylo)

 S3method(fortify,obkData)

-S3method(fortify,paml_rst)

-S3method(fortify,phangorn)

-S3method(fortify,phylip)

 S3method(fortify,phylo)

 S3method(fortify,phylo4)

 S3method(fortify,phylo4d)

 S3method(fortify,phyloseq)

-S3method(fortify,r8s)

 S3method(fortify,treedata)

 S3method(identify,gg)

 S3method(print,beastList)

@@ -195,9 +187,10 @@ importFrom(scales,alpha)

 importFrom(tibble,as_data_frame)

 importFrom(tibble,data_frame)

 importFrom(tidyr,gather)

+importFrom(treeio,Nnode)

+importFrom(treeio,Ntip)

 importFrom(treeio,as.phylo)

 importFrom(treeio,as.treedata)

-importFrom(treeio,get.placements)

 importFrom(treeio,groupClade)

 importFrom(treeio,groupOTU)

 importFrom(utils,modifyList)

@@ -1,3 +1,7 @@

+CHANGES IN VERSION 1.11.3

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

+ o remove paml_rst, codeml_mlc, codeml and jplace fortify methods according to the change of treeio (v = 1.3.3) <2017-12-07, Thu>

+

 CHANGES IN VERSION 1.11.2

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

  o keep tree order (previously using postorder) <2017-12-06-Wed>

@@ -1,4 +1,3 @@

-

 ##' collapse binary tree to polytomy by applying 'fun' to 'feature'

 ##'

 ##'

@@ -19,11 +18,11 @@ as.polytomy <- function(tree, feature, fun) {

     phylo <- get.tree(tree)

     if (feature == 'node.label') {

-        feat <- df[!df$isTip, 'label']

+        feat <- df$label[!df$isTip]

     } else if (feature == 'tip.label') {

-        feat <- df[df$isTip, 'label']

+        feat <- df$label[df$isTip]

     } else {

-        feat <- df[, feature]

+        feat <- df[[feature]]

     }

     idx <- which(fun(feat))

@@ -133,12 +133,12 @@ expand <- function(tree_view=NULL, node) {

     root <- which(df$node == df$parent)

     pp <- node

     while(any(pp != root)) {

-        df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

-        pp <- df[pp, "parent"]

+        df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        pp <- df$parent[pp]

     }

     j <- getChild.df(df, pp)

     j <- j[j!=pp]

-    df[pp, "y"] <- mean(df[j, "y"])

+    df[pp, "y"] <- mean(df$y[j])

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

@@ -166,17 +166,17 @@ rotate <- function(tree_view=NULL, node) {

     tip <- sp[df$isTip[sp_idx]]

     sp.df <- df[sp_idx,]

     ii <- with(sp.df, match(tip, node))

-    jj <- ii[order(sp.df[ii, "y"])]

-    sp.df[jj,"y"] <- rev(sp.df[jj, "y"])

+    jj <- ii[order(sp.df$y[ii])]

+    sp.df[jj,"y"] <- rev(sp.df$y[jj])

     sp.df[-jj, "y"] <- NA

     sp.df <- re_assign_ycoord_df(sp.df, tip)

     df[sp_idx, "y"] <- sp.df$y

     ## df$node == node is TRUE when node was root

-    df[df$node == node, "y"] <- mean(df[df$parent == node & df$node != node, "y"])

+    df[df$node == node, "y"] <- mean(df$y[df$parent == node & df$node != node])

     pnode <- df$parent[df$node == node]

     if (pnode != node && !is.na(pnode)) {

-        df[df$node == pnode, "y"] <- mean(df[df$parent == pnode, "y"])

+        df[df$node == pnode, "y"] <- mean(df$y[df$parent == pnode])

     }

     tree_view$data <- calculate_angle(df)

@@ -275,9 +275,9 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     ## new_span <- span * scale

     old.sp.df <- sp.df

-    sp.df$y <- df[node, "y"] + (sp.df$y - df[node, "y"]) * scale

+    sp.df$y <- df$y[node] + (sp.df$y - df$y[node]) * scale

     if (! vertical_only) {

-        sp.df$x <- df[node, "x"] + (sp.df$x - df[node, "x"]) * scale

+        sp.df$x <- df$x[node] + (sp.df$x - df$x[node]) * scale

     }

     scale_diff.up <- max(sp.df$y) - max(old.sp.df$y)

@@ -285,12 +285,12 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     ii <- df$y > max(old.sp.df$y)

     if (sum(ii) > 0) {

-        df[ii, "y"] <- df[ii, "y"] + scale_diff.up

+        df[ii, "y"] <- df$y[ii] + scale_diff.up

     }

     jj <- df$y < min(old.sp.df$y)

     if (sum(jj) > 0) {

-        df[jj, "y"] <- df[jj, "y"] + scale_diff.lw

+        df[jj, "y"] <- df$y[jj] + scale_diff.lw

     }

     df[sp,] <- sp.df

@@ -320,13 +320,13 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

 reassign_y_from_node_to_root <- function(df, node) {

     root <- which(df$node == df$parent)

-    pp <- df[node, "parent"]

+    pp <- df$parent[node]

     while(any(pp != root)) {

-        df[pp, "y"] <- mean(df[getChild.df(df, pp), "y"])

-        pp <- df[pp, "parent"]

+        df[pp, "y"] <- mean(df$y[getChild.df(df, pp)])

+        pp <- df$parent[pp]

     }

     j <- getChild.df(df, pp)

     j <- j[j!=pp]

-    df[pp, "y"] <- mean(df[j, "y"])

+    df[pp, "y"] <- mean(df$y[j])

     return(df)

 }

@@ -220,169 +220,132 @@ rm.singleton.newick <- function(nwk, outfile = NULL) {

 ## }

-##' @method fortify codeml

-##' @export

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

-                           layout        = "rectangular",

-                           yscale        = "none",

-                           ladderize     = TRUE,

-                           right         = FALSE,

-                           branch.length = "mlc.branch.length",

-                           ndigits       = NULL,

-                           mrsd          = NULL,

-                           ...) {

-

-    dNdS <- model@mlc@dNdS

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

-        message("branch.length setting to mlc.branch.length by default...")

-        branch.length <- "mlc.branch.length"

-    }

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

-                        c("none",

-                          "mlc.branch.length",

-                          "rst.branch.length",

-                          colnames(dNdS)[-c(1,2)])

-                        )

-

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

-        phylo <- get.tree(model@rst)

-    } else {

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

-            length <- "branch.length"

-        }

-        mlc <- set_branch_length(model@mlc, length)

-        phylo <- get.tree(mlc)

-    }

-

-    df <- fortify(phylo, data, layout, ladderize, right,

-                  branch.length=length, mrsd=mrsd, ...)

-

-    res <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

-    df <- merge_phylo_anno.paml_rst(res, model@rst)

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

-

-    append_extraInfo(df, model)

-}

-

-

-##' @method fortify codeml_mlc

-##' @export

-fortify.codeml_mlc <- 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 <- get.tree(model)

-    df <- fortify(phylo, data, layout, ladderize, right,

-                  branch.length=branch.length, mrsd=mrsd, ...)

-

-    dNdS <- model@dNdS

-

-    df <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

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

-

-    append_extraInfo(df, model)

-}

+## ##' @method fortify codeml

+## ##' @export

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

+##                            layout        = "rectangular",

+##                            yscale        = "none",

+##                            ladderize     = TRUE,

+##                            right         = FALSE,

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

+##                            ndigits       = NULL,

+##                            mrsd          = NULL,

+##                            ...) {

+

+##     dNdS <- model@mlc@dNdS

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

+##         message("branch.length setting to mlc.branch.length by default...")

+##         branch.length <- "mlc.branch.length"

+##     }

+##     length <- match.arg(branch.length,

+##                         c("none",

+##                           "mlc.branch.length",

+##                           "rst.branch.length",

+##                           colnames(dNdS)[-c(1,2)])

+##                         )

+

+##     if (length == "rst.branch.length") {

+##         phylo <- get.tree(model@rst)

+##     } else {

+##         if (length == "mlc.branch.length") {

+##             length <- "branch.length"

+##         }

+##         mlc <- set_branch_length(model@mlc, length)

+##         phylo <- get.tree(mlc)

+##     }

-merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

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

-        idx <- which(! colnames(dNdS) %in% c("node", "parent"))

-        for (ii in idx) {

-            if (is.numeric(dNdS[, ii])) {

-                dNdS[, ii] <- round(dNdS[,ii], ndigits)

-            }

-        }

-    }

+##     df <- fortify(phylo, data, layout, ladderize, right,

+##                   branch.length=length, mrsd=mrsd, ...)

-    res <- merge(df, dNdS,

-                 by.x  = c("node", "parent"),

-                 by.y  = c("node", "parent"),

-                 all.x = TRUE)

+##     res <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

+##     df <- merge_phylo_anno.paml_rst(res, model@rst)

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

-    res[match(df$node, res$node),]

-}

+##     append_extraInfo(df, model)

+## }

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

-                                layout        = "rectangular",

-                                ladderize     = TRUE,

-                                right         = FALSE,

-                                branch.length = "branch.length",

-                                ...) {

-}

+## ##' @method fortify codeml_mlc

+## ##' @export

+## fortify.codeml_mlc <- 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 <- get.tree(model)

+##     df <- fortify(phylo, data, layout, ladderize, right,

+##                   branch.length=branch.length, mrsd=mrsd, ...)

+##     dNdS <- model@dNdS

-##' @method fortify paml_rst

-##' @export

-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, ...)

+##     df <- merge_phylo_anno.codeml_mlc(df, dNdS, ndigits)

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

-    append_extraInfo(df, model)

-}

+##     append_extraInfo(df, model)

+## }

-merge_phylo_anno.paml_rst <- function(df, model) {

-    types <- get.fields(model)

-    types <- types[grepl('subs', types)]

-    for (type in types) {

-        anno <- get.subs(model, type=type)

-        colnames(anno)[2] <- type

-        df <- df %add2% anno

-    }

-    return(df)

-}

+## merge_phylo_anno.codeml_mlc <- function(df, dNdS, ndigits = NULL) {

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

+##         idx <- which(! colnames(dNdS) %in% c("node", "parent"))

+##         for (ii in idx) {

+##             if (is.numeric(dNdS[, ii])) {

+##                 dNdS[, ii] <- round(dNdS[,ii], ndigits)

+##             }

+##         }

+##     }

+##     res <- merge(df, dNdS,

+##                  by.x  = c("node", "parent"),

+##                  by.y  = c("node", "parent"),

+##                  all.x = TRUE)

-##' @method fortify phangorn

-##' @export

-fortify.phangorn <- fortify.paml_rst

+##     res[match(df$node, res$node),]

+## }

-##' @method fortify hyphy

-##' @export

-fortify.hyphy <- fortify.paml_rst

+## ##' @method fortify paml_rst

+## ##' @export

+## 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, ...)

+##     append_extraInfo(df, model)

+## }

-##' @method fortify jplace

-##' @importFrom ape read.tree

-##' @importFrom treeio get.placements

-##' @export

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

-                           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")

+## merge_phylo_anno.paml_rst <- function(df, model) {

+##     types <- get.fields(model)

+##     types <- types[grepl('subs', types)]

+##     for (type in types) {

+##         anno <- get.subs(model, type=type)

+##         colnames(anno)[2] <- type

+##         df <- df %add2% anno

+##     }

+##     return(df)

+## }

-    nplace <- split(place, place$edge_num) %>% lapply(nrow)

-    nplace.df <- data.frame(edgeNum = names(nplace), nplace=unlist(nplace))

-    ## df <- merge(df, place, by.x="edgeNum", by.y="edge_num", all.x=TRUE)

-    df <- merge(df, nplace.df, by.x="edgeNum", by.y="edgeNum", all.x=TRUE)

+## ##' @method fortify phangorn

+## ##' @export

+## fortify.phangorn <- fortify.paml_rst

-    df$nplace[is.na(df$nplace)] <- 0

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

+## ##' @method fortify hyphy

+## ##' @export

+## fortify.hyphy <- fortify.paml_rst

-    append_extraInfo(df, model)

-}

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

     if (yscale == "none") {

@@ -447,72 +410,72 @@ fortify.phylo4d <- function(model, data,

-##' fortify a phylo to data.frame

-##'

-##'

-##' @rdname fortify

-##' @title fortify

-##' @param model phylo object

-##' @param data not use here

-##' @param layout layout

-##' @param ladderize ladderize, logical

-##' @param right logical

-##' @param mrsd most recent sampling date

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

-##' @param ... additional parameter

-##' @return data.frame

-##' @importFrom ape ladderize

-##' @importFrom ape reorder.phylo

-##' @importFrom ggplot2 fortify

-##' @method fortify phylo

-##' @export

-##' @author Yu Guangchuang

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

-                          layout    = "rectangular",

-                          ladderize = TRUE,

-                          right     = FALSE,

-                          mrsd      = NULL,

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

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

-    tree <- model

-

-    if (ladderize == TRUE) {

-        tree <- ladderize(tree, right=right)

-    }

+## ##' fortify a phylo to data.frame

+## ##'

+## ##'

+## ##' @rdname fortify

+## ##' @title fortify

+## ##' @param model phylo object

+## ##' @param data not use here

+## ##' @param layout layout

+## ##' @param ladderize ladderize, logical

+## ##' @param right logical

+## ##' @param mrsd most recent sampling date

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

+## ##' @param ... additional parameter

+## ##' @return data.frame

+## ##' @importFrom ape ladderize

+## ##' @importFrom ape reorder.phylo

+## ##' @importFrom ggplot2 fortify

+## ##' @method fortify phylo

+## ##' @export

+## ##' @author Yu Guangchuang

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

+##                           layout    = "rectangular",

+##                           ladderize = TRUE,

+##                           right     = FALSE,

+##                           mrsd      = NULL,

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

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

+##     tree <- model

+

+##     if (ladderize == TRUE) {

+##         tree <- ladderize(tree, right=right)

+##     }

-    if (! is.null(tree$edge.length)) {

-        if (anyNA(tree$edge.length)) {

-            warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...")

-            tree$edge.length <- NULL

-        }

-    }

+##     if (! is.null(tree$edge.length)) {

+##         if (anyNA(tree$edge.length)) {

+##             warning("'edge.length' contains NA values...\n## setting 'edge.length' to NULL automatically when plotting the tree...")

+##             tree$edge.length <- NULL

+##         }

+##     }

-    df <- as.data.frame(tree, layout=layout, ...)

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

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

-    rownames(df) <- df$node

-    cn <- colnames(df)

-    colnames(df)[grep("length", cn)] <- "branch.length"

-    if(layout == "slanted") {

-        df <- add_angle_slanted(df)

-    }

-    aa <- names(attributes(tree))

-    group <- aa[ ! aa %in% c("names", "class", "order", "reroot", "node_map")]

-    if (length(group) > 0) {

-        for (group_ in group) {

-            ## groupOTU & groupClade

-            group_info <- attr(tree, group_)

-            if (length(group_info) == nrow(df)) {

-                df[, group_] <- group_info

-            }

-        }

-    }

+##     df <- as.data.frame(tree, layout=layout, ...)

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

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

+##     rownames(df) <- df$node

+##     cn <- colnames(df)

+##     colnames(df)[grep("length", cn)] <- "branch.length"

+##     if(layout == "slanted") {

+##         df <- add_angle_slanted(df)

+##     }

+##     aa <- names(attributes(tree))

+##     group <- aa[ ! aa %in% c("names", "class", "order", "reroot", "node_map")]

+##     if (length(group) > 0) {

+##         for (group_ in group) {

+##             ## groupOTU & groupClade

+##             group_info <- attr(tree, group_)

+##             if (length(group_info) == nrow(df)) {

+##                 df[, group_] <- group_info

+##             }

+##         }

+##     }

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

-        df <- scaleX_by_time_from_mrsd(df, mrsd, as.Date)

-    }

-    return(df)

-}

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

+##         df <- scaleX_by_time_from_mrsd(df, mrsd, as.Date)

+##     }

+##     return(df)

+## }

 ##' convert phylo to data.frame

 ##'

@@ -592,29 +555,6 @@ as.data.frame.phylo_ <- function(x, layout="rectangular",

     return(res)

 }

-## ##' @method fortify nhx

-## ##' @export

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

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

-##     df <- fortify(get.tree(model), layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

-##     df <- merge(df, model@nhx_tags, by.x="node", by.y="node", all.x=TRUE)

-##     append_extraInfo(df, model)

-## }

-

-

-## ##' @method fortify raxml

-## ##' @export

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

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

-##     df <- fortify(get.tree(model), layout=layout, ladderize=ladderize, right=right, mrsd=mrsd, ...)

-##     df <- merge(df, model@bootstrap, by.x="node", by.y="node", all.x=TRUE)

-##     append_extraInfo(df, model)

-## }

-

-## ##' @method fortify apeBootstrap

-## ##' @export

-## fortify.apeBootstrap <- fortify.raxml

-

 ##' @method fortify multiPhylo

 ##' @export

@@ -633,38 +573,9 @@ fortify.multiPhylo <-  function(model, data,

     df <- do.call("rbind", df.list)

     df$.id <- rep(names(df.list), times=sapply(df.list, nrow))

     df$.id <- factor(df$.id, levels=names(df.list))

-

-    ## nNode <- sapply(df.list, nrow)

-    ## nNode2 <- cumsum(c(0, nNode[-length(nNode)]))

-    ## df$parent <- df$parent + rep(nNode2, times=nNode)

     return(df)

 }

-##' @method fortify phylip

-##' @export

-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",

-                        ladderize     = TRUE,

-                        right         = FALSE,

-                        branch.length = "TREE",

-                        mrsd          = NULL, ...) {

-    trees <- get.tree(model)

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

-    phylo <- trees[[branch.length]]

-    fortify(phylo, layout=layout, ladderize = ladderize, right=right, mrsd=mrsd, ...)

-}

 ##' @method fortify obkData

 ##' @export

@@ -94,16 +94,16 @@ groupClade.ggtree <- function(object, nodes, group_name) {

     df <- object$data

     df[, group_name] <- 0

     for (node in nodes) {

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

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

     }

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

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

     object$data <- df

     return(object)

 }

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

+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

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

     return(df)

 }

@@ -191,30 +191,30 @@ setMethod("groupOTU", signature(object="ggtree"),

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

     df <- object$data

-    df[, group_name] <- 0

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

+    df[[group_name]] <- 0

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

     return(object)

 }

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

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

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

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

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

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

         }

     } else {

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

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

     }

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

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

     return(df)

 }

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

+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

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

     if (length(focus) == 1) {

         hit <- match(focus, df$node)

@@ -231,7 +231,7 @@ gfocus.df <- function(df, focus, group_name, focus_label=NULL, overlap="overwrit

         hit <- match(foc, df$node)

     }

-    foc <- df[, group_name]

+    foc <- df[[group_name]]

     if (overlap == "origin") {

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

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

@@ -78,12 +78,12 @@ setMethod("gzoom", signature(object="ggtree"),

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

 ##           })

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

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

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

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

-          })

+## ##' @rdname gzoom-methods

+## ##' @exportMethod gzoom

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

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

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

+##           })

 ##' zoom selected subtree

 ##'

@@ -96,12 +96,12 @@ setMethod("gzoom", signature(object="treedata"),

           })

-##' @rdname gzoom-methods

-##' @exportMethod gzoom

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

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

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

-          })

+## ##' @rdname gzoom-methods

+## ##' @exportMethod gzoom

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

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

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

+##           })

 ##' @rdname gzoom-methods

@@ -18,12 +18,12 @@ setMethod("scale_color", signature(object="treedata"),

               scale_color_(object, by, ...)

           })

-##' @rdname scale_color-methods

-##' @exportMethod scale_color

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

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

-              scale_color_(object, by, ...)

-          })

+## ##' @rdname scale_color-methods

+## ##' @exportMethod scale_color

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

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

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

+##           })

 ##' @rdname scale_color-methods

deleted file mode 100644

@@ -1,175 +0,0 @@

-## ##' @rdname show-methods

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

-## ##' @exportMethod show

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

-##           function(object) {

-##               cat("'beast' S4 object that stored information of\n\t",

-##                   paste0("'", object@file, "'.\n\n"))

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

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

-##               cat("\nwith the following features available:\n")

-##               print_fields(object)

-##           })

-

-## ##' @rdname show-methods

-## ##' @exportMethod show

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

-##           function(object) {

-##               cat("'codeml' S4 object that stored information of\n\t",

-##                   paste0("'", object@rst@rstfile, "' and \n\t'",

-##                          object@mlc@mlcfile, "'."),

-##                   "\n\n")

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

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

-##               cat("\nwith the following features available:\n")

-##               print_fields(object, len=4)

-##           })

-

-## ##' @rdname show-methods

-## ##' @exportMethod show

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

-##           function(object) {

-##               cat("'codeml_mlc' S4 object that stored information of\n\t",

-##                   paste0("'", object@mlcfile, "'."),

-##                   "\n\n")

-

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

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

-

-##               cat("\nwith the following features available:\n")

-##               cat("\t", paste0("'",

-##                                  paste(get.fields(object), collapse="',\t'"),

-##                                  "'."),

-##                   "\n")

-##           }

-##           )

-

-## ##' show method for \code{jplace} instance

-## ##'

-## ##'

-## ##' @name show

-## ##' @docType methods

-## ##' @rdname show-methods

-## ##'

-## ##' @title show method

-## ##' @param object one of \code{jplace}, \code{beast} object

-## ##' @return print info

-## ##' @importFrom methods show

-## ##' @exportMethod show

-## ##' @usage show(object)

-## ##' @author Guangchuang Yu \url{http://ygc.name}

-## ##' @examples

-## ##' jp <- system.file("extdata", "sample.jplace", package="ggtree")

-## ##' jp <- read.jplace(jp)

-## ##' show(jp)

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

-##           function(object) {

-##               cat("'jplace' S4 object that stored information of\n\t",

-##                   paste0("'", object@file, "'."),

-##                   "\n\n")

-

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

-

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

-##               phylo$node.label <- NULL

-##               phylo$tip.label %<>% gsub("\\@\\d+", "", .)

-

-##               print.phylo(phylo)

-

-##               cat("\nwith the following features availables:\n")

-##               cat("\t", paste0("'",

-##                                paste(get.fields(object), collapse="',\t'"),

-##                                "'."),

-##                   "\n")

-##           }

-##           )

-

-

-## ##' @rdname show-methods

-## ##' @exportMethod show

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

-##           function(object) {

-##               cat("'nhx' S4 object that stored information of\n\t",

-##                   paste0("'", object@file, "'.\n\n"))

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

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

-##               cat("\nwith the following features available:\n")

-##               print_fields(object)

-##           })