@@ -1,5 +1,12 @@

+CHANGES IN VERSION 1.3.9

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

+ o viewClade, scaleClade, collapse, expand, rotate, flip, get_taxa_name and scale_x_ggtree accepts input tree_view=NULL.

+   these function will access the last plot if tree_view=NULL. <2016-01-13, Wed>

+   + > ggtree(rtree(30)); viewClade(node=35) works. no need to pipe.

+ 

 CHANGES IN VERSION 1.3.8

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

+ o add example of viewClade in 'Tree Manipulation' vignette <2016-01-13, Wed>

  o add viewClade function <2016-01-12, Tue>

  o support obkData object defined by OutbreakTools <2016-01-12, Tue>

  o update vignettes <2016-01-07, Thu>

@@ -13,7 +20,7 @@ CHANGES IN VERSION 1.3.7

    + 00 ggtree <2015-12-29, Tue>

    + 01 tree data import <2015-12-28, Mon>

    + 02 tree visualization <2015-12-28, Mon>

-   + 03 tree view manipulation <2015-12-28, Mon>

+   + 03 tree manipulation <2015-12-28, Mon>

    + 04 tree annotation <2015-12-29, Tue>

 CHANGES IN VERSION 1.3.6

new file mode 100644

@@ -0,0 +1,285 @@

+##' get taxa name of a selected node

+##'

+##' 

+##' @title get_taxa_name

+##' @param tree_view tree view

+##' @param node node

+##' @return taxa name vector

+##' @export

+##' @author Guangchuang Yu

+get_taxa_name <- function(tree_view=NULL, node) {

+    tree_view %<>% get_tree_view

+    

+    df <- tree_view$data

+    sp <- get.offspring.df(df, node)

+    res <- df[sp, "label"]

+    return(res[df[sp, "isTip"]])

+}

+

+

+

+

+##' view a clade of tree

+##'

+##' 

+##' @title viewClade

+##' @param tree_view full tree view 

+##' @param node internal node number

+##' @param xmax_adjust adjust xmax

+##' @return clade plot

+##' @export

+##' @author Guangchuang Yu

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

+    tree_view %<>% get_tree_view

+    

+    cpos <- get_clade_position(tree_view, node=node)

+    with(cpos, tree_view+xlim(xmin, xmax*1.01 + xmax_adjust) + ylim(ymin, ymax))

+}

+

+

+##' collapse a clade

+##'

+##' 

+##' @title collapse

+##' @param tree_view tree view 

+##' @param node clade node

+##' @return tree view

+##' @export

+##' @seealso expand

+##' @author Guangchuang Yu

+collapse <- function(tree_view=NULL, node) {

+    tree_view %<>% get_tree_view

+    

+    df <- tree_view$data

+    sp <- get.offspring.df(df, node)

+    sp.df <- df[sp,]

+    df[node, "isTip"] <- TRUE

+    sp_y <- range(sp.df$y)

+    ii <- which(df$y > max(sp_y))

+    if (length(ii)) {

+        df$y[ii] <- df$y[ii] - diff(sp_y)

+    }

+    df$y[node] <- min(sp_y)

+

+    df[sp, "x"] <- NA

+    df[sp, "y"] <- NA

+    

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

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

+    while(any(pp != root)) {

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

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

+    }

+    j <- getChild.df(df, pp)

+    j <- j[j!=pp]

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

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

+

+    tree_view$data <- df

+    clade <- paste0("clade_", node)

+    attr(tree_view, clade) <- sp.df

+    tree_view

+}

+

+##' expand collased clade

+##'

+##' 

+##' @title expand

+##' @param tree_view tree view

+##' @param node clade node

+##' @return tree view

+##' @export

+##' @seealso collapse

+##' @author Guangchuang Yu

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

+    tree_view %<>% get_tree_view

+    

+    clade <- paste0("clade_", node)

+    sp.df <- attr(tree_view, clade)

+    if (is.null(sp.df)) {

+        return(tree_view)

+    }

+    df <- tree_view$data

+    df[node, "isTip"] <- FALSE

+    sp_y <- range(sp.df$y)

+    ii <- which(df$y > df$y[node])

+    df[ii, "y"] <- df[ii, "y"] + diff(sp_y)

+    

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

+    df[sp.df$node,] <- sp.df

+

+    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"]

+    }

+    j <- getChild.df(df, pp)

+    j <- j[j!=pp]

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

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

+    

+    tree_view$data <- df

+    attr(tree_view, clade) <- NULL

+    tree_view

+}

+

+##' rotate 180 degree of a selected branch

+##'

+##' 

+##' @title rotate

+##' @param tree_view tree view 

+##' @param node selected node

+##' @return ggplot2 object

+##' @export

+##' @author Guangchuang Yu

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

+    tree_view %<>% get_tree_view

+    

+    df <- tree_view$data

+    sp <- get.offspring.df(df, node)

+    sp_idx <- with(df, match(sp, 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"])

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

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

+

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

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

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

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

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

+    }

+    tree_view$data <- df

+    tree_view

+}

+

+

+

+##' flip position of two selected branches

+##'

+##' 

+##' @title flip

+##' @param tree_view tree view 

+##' @param node1 node number of branch 1

+##' @param node2 node number of branch 2

+##' @return ggplot2 object

+##' @export

+##' @author Guangchuang Yu

+flip <- function(tree_view=NULL, node1, node2) {

+    tree_view %<>% get_tree_view

+    

+    df <- tree_view$data

+    p1 <- with(df, parent[node == node1])

+    p2 <- with(df, parent[node == node2])

+

+    if (p1 != p2) {

+        stop("node1 and node2 should share a same parent node...")

+    }

+

+    sp1 <- c(node1, get.offspring.df(df, node1))

+    sp2 <- c(node2, get.offspring.df(df, node2))

+

+    sp1.df <- df[sp1,]

+    sp2.df <- df[sp2,]

+

+    min_y1 <- min(sp1.df$y)

+    min_y2 <- min(sp2.df$y)

+

+    if (min_y1 < min_y2) {

+        tmp <- sp1.df

+        sp1.df <- sp2.df

+        sp2.df <- tmp

+        tmp <- sp1

+        sp1 <- sp2

+        sp2 <- tmp

+    }

+

+    min_y1 <- min(sp1.df$y)

+    min_y2 <- min(sp2.df$y)

+

+    space <- min(sp1.df$y) - max(sp2.df$y)

+    sp1.df$y <- sp1.df$y - abs(min_y1 - min_y2)

+    sp2.df$y <- sp2.df$y + max(sp1.df$y) + space - min(sp2.df$y)

+

+    df[sp1, "y"] <- sp1.df$y

+    df[sp2, "y"] <- sp2.df$y

+

+    anc <- getAncestor.df(df, node1)

+    ii <- match(anc, df$node)

+    df[ii, "y"] <- NA

+    currentNode <- unlist(as.vector(sapply(anc, getChild.df, df=df)))

+    currentNode <- currentNode[!currentNode %in% anc]

+    

+    tree_view$data <- re_assign_ycoord_df(df, currentNode)

+    tree_view

+}

+

+

+##' scale clade

+##'

+##' 

+##' @title scaleClade

+##' @param tree_view tree view

+##' @param node clade node

+##' @param scale scale

+##' @param vertical_only logical. If TRUE, only vertical will be scaled.

+##' If FALSE, the clade will be scaled vertical and horizontally.

+##' TRUE by default.

+##' @return tree view

+##' @export

+##' @author Guangchuang Yu

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

+    tree_view %<>% get_tree_view

+    

+    if (scale == 1) {

+        return(tree_view)

+    }

+    

+    df <- tree_view$data

+    sp <- get.offspring.df(df, node)

+    sp.df <- df[sp,]

+    

+    ## sp_nr <- nrow(sp.df)

+    ## span <- diff(range(sp.df$y))/sp_nr

+    

+    ## new_span <- span * scale

+    old.sp.df <- sp.df

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

+    if (vertical_only == FALSE) {

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

+    }

+    

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

+    scale_diff.lw <- min(sp.df$y) - min(old.sp.df$y)

+    

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

+    if (sum(ii) > 0) {

+        df[ii, "y"] <- df[ii, "y"] + 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[sp,] <- sp.df

+    

+    if (! "scale" %in% colnames(df)) {

+        df$scale <- 1

+    }

+    df[sp, "scale"] <- df[sp, "scale"] * scale

+

+    ## re-calculate branch mid position

+    df <- calculate_branch_mid(df)

+    

+    tree_view$data <- df

+    tree_view

+}

@@ -143,256 +143,8 @@ geom_tree <- function(layout="rectangular", ...) {

-##' scale clade

-##'

-##' 

-##' @title scaleClade

-##' @param tree_view tree view

-##' @param node clade node

-##' @param scale scale

-##' @param vertical_only logical. If TRUE, only vertical will be scaled.

-##' If FALSE, the clade will be scaled vertical and horizontally.

-##' TRUE by default.

-##' @return tree view

-##' @export

-##' @author Guangchuang Yu

-scaleClade <- function(tree_view, node, scale=1, vertical_only=TRUE) {

-    if (scale == 1) {

-        return(tree_view)

-    }

-    

-    df <- tree_view$data

-    sp <- get.offspring.df(df, node)

-    sp.df <- df[sp,]

-    

-    ## sp_nr <- nrow(sp.df)

-    ## span <- diff(range(sp.df$y))/sp_nr

-    

-    ## new_span <- span * scale

-    old.sp.df <- sp.df

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

-    if (vertical_only == FALSE) {

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

-    }

-    

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

-    scale_diff.lw <- min(sp.df$y) - min(old.sp.df$y)

-    

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

-    if (sum(ii) > 0) {

-        df[ii, "y"] <- df[ii, "y"] + 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[sp,] <- sp.df

-    

-    if (! "scale" %in% colnames(df)) {

-        df$scale <- 1

-    }

-    df[sp, "scale"] <- df[sp, "scale"] * scale

-

-    ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

-    

-    tree_view$data <- df

-    tree_view

-}

-

-

-##' flip position of two selected branches

-##'

-##' 

-##' @title flip

-##' @param tree_view tree view 

-##' @param node1 node number of branch 1

-##' @param node2 node number of branch 2

-##' @return ggplot2 object

-##' @export

-##' @author Guangchuang Yu

-flip <- function(tree_view, node1, node2) {

-    df <- tree_view$data

-    p1 <- with(df, parent[node == node1])

-    p2 <- with(df, parent[node == node2])

-

-    if (p1 != p2) {

-        stop("node1 and node2 should share a same parent node...")

-    }

-

-    sp1 <- c(node1, get.offspring.df(df, node1))

-    sp2 <- c(node2, get.offspring.df(df, node2))

-

-    sp1.df <- df[sp1,]

-    sp2.df <- df[sp2,]

-

-    min_y1 <- min(sp1.df$y)

-    min_y2 <- min(sp2.df$y)

-

-    if (min_y1 < min_y2) {

-        tmp <- sp1.df

-        sp1.df <- sp2.df

-        sp2.df <- tmp

-        tmp <- sp1

-        sp1 <- sp2

-        sp2 <- tmp

-    }

-

-    min_y1 <- min(sp1.df$y)

-    min_y2 <- min(sp2.df$y)

-

-    space <- min(sp1.df$y) - max(sp2.df$y)

-    sp1.df$y <- sp1.df$y - abs(min_y1 - min_y2)

-    sp2.df$y <- sp2.df$y + max(sp1.df$y) + space - min(sp2.df$y)

-

-    df[sp1, "y"] <- sp1.df$y

-    df[sp2, "y"] <- sp2.df$y

-

-    anc <- getAncestor.df(df, node1)

-    ii <- match(anc, df$node)

-    df[ii, "y"] <- NA

-    currentNode <- unlist(as.vector(sapply(anc, getChild.df, df=df)))

-    currentNode <- currentNode[!currentNode %in% anc]

-    

-    tree_view$data <- re_assign_ycoord_df(df, currentNode)

-    tree_view

-}

-

-##' rotate 180 degree of a selected branch

-##'

-##' 

-##' @title rotate

-##' @param tree_view tree view 

-##' @param node selected node

-##' @return ggplot2 object

-##' @export

-##' @author Guangchuang Yu

-rotate <- function(tree_view, node) {

-    df <- tree_view$data

-    sp <- get.offspring.df(df, node)

-    sp_idx <- with(df, match(sp, 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"])

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

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

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

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

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

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

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

-    }

-    tree_view$data <- df

-    tree_view

-}

-re_assign_ycoord_df <- function(df, currentNode) {

-    while(any(is.na(df$y))) {

-        pNode <- with(df, parent[match(currentNode, node)]) %>% unique

-        idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode)))

-        newNode <- pNode[idx]

-        ## newNode <- newNode[is.na(df[match(newNode, df$node), "y"])]

-        

-        df[match(newNode, df$node), "y"] <- sapply(newNode, function(i) {

-            with(df, mean(y[parent == i], na.rm = TRUE))

-        })

-        traced_node <- as.vector(sapply(newNode, function(i) with(df, node[parent == i])))

-        currentNode <- c(currentNode[! currentNode %in% traced_node], newNode)

-    }

-    return(df)

-}

-

-##' collapse a clade

-##'

-##' 

-##' @title collapse

-##' @param tree_view tree view 

-##' @param node clade node

-##' @return tree view

-##' @export

-##' @seealso expand

-##' @author Guangchuang Yu

-collapse <- function(tree_view, node) {

-    df <- tree_view$data

-    sp <- get.offspring.df(df, node)

-    sp.df <- df[sp,]

-    df[node, "isTip"] <- TRUE

-    sp_y <- range(sp.df$y)

-    ii <- which(df$y > max(sp_y))

-    if (length(ii)) {

-        df$y[ii] <- df$y[ii] - diff(sp_y)

-    }

-    df$y[node] <- min(sp_y)

-

-    df[sp, "x"] <- NA

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

-    

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

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

-    while(any(pp != root)) {

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

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

-    }

-    j <- getChild.df(df, pp)

-    j <- j[j!=pp]

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

-

-    ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

-

-    tree_view$data <- df

-    clade <- paste0("clade_", node)

-    attr(tree_view, clade) <- sp.df

-    tree_view

-}

-

-##' expand collased clade

-##'

-##' 

-##' @title expand

-##' @param tree_view tree view

-##' @param node clade node

-##' @return tree view

-##' @export

-##' @seealso collapse

-##' @author Guangchuang Yu

-expand <- function(tree_view, node) {

-    clade <- paste0("clade_", node)

-    sp.df <- attr(tree_view, clade)

-    if (is.null(sp.df)) {

-        return(tree_view)

-    }

-    df <- tree_view$data

-    df[node, "isTip"] <- FALSE

-    sp_y <- range(sp.df$y)

-    ii <- which(df$y > df$y[node])

-    df[ii, "y"] <- df[ii, "y"] + diff(sp_y)

-    

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

-    df[sp.df$node,] <- sp.df

-

-    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"]

-    }

-    j <- getChild.df(df, pp)

-    j <- j[j!=pp]

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

-

-    ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

-    

-    tree_view$data <- df

-    attr(tree_view, clade) <- NULL

-    tree_view

-}

 ##' add colorbar legend

 ##'

@@ -460,23 +212,6 @@ add_colorbar <- function(p, color, x=NULL, ymin=NULL, ymax=NULL, font.size=4) {

 }

-##' get taxa name of a selected node

-##'

-##' 

-##' @title get_taxa_name

-##' @param tree_view tree view

-##' @param node node

-##' @return taxa name vector

-##' @export

-##' @author Guangchuang Yu

-get_taxa_name <- function(tree_view, node) {

-    df <- tree_view$data

-    sp <- get.offspring.df(df, node)

-    res <- df[sp, "label"]

-    return(res[df[sp, "isTip"]])

-}

-

-

@@ -213,7 +213,7 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

 ##'

 ##' 

 ##' @title scale_x_ggtree

-##' @param p tree view

+##' @param tree_view tree view

 ##' @param breaks breaks for tree

 ##' @param labels lables for corresponding breaks

 ##' @return tree view

@@ -221,7 +221,9 @@ msaplot <- function(p, fasta, offset=0, width=1, color=NULL, window=NULL){

 ##' @importFrom ggplot2 scale_x_date

 ##' @export

 ##' @author Guangchuang Yu

-scale_x_ggtree <- function(p, breaks=NULL, labels=NULL) {

+scale_x_ggtree <- function(tree_view, breaks=NULL, labels=NULL) {

+    p <- get_tree_view(tree_view)

+    

     mrsd <- attr(p, "mrsd")

     if (!is.null(mrsd) && class(p$data$x) == "Date") {

         x <- Date2decimal(p$data$x)

new file mode 100644

@@ -0,0 +1,19 @@

+`%add%` <- function(p, data) {

+    p$data <- p$data %add2% data

+    return(p)

+}

+

+`%add2%` <- function(d1, d2) {

+    if ("node" %in% colnames(d2)) {

+        cn <- colnames(d2)

+        ii <- which(cn %in% c("node", cn[!cn %in% colnames(d1)]))

+        d2 <- d2[, ii]

+        dd <- merge(d1, d2, by.x="node", by.y="node", all.x=TRUE)

+    } else {

+        d2[,1] <- as.character(d2[,1])

+        dd <- merge(d1, d2, by.x="label", by.y=1, all.x=TRUE)

+    }

+    dd <- dd[match(d1$node, dd$node),]

+    return(dd)

+}

+

@@ -870,3 +870,20 @@ set_branch_length <- function(tree_object, branch.length) {

     return(phylo)

 }

+

+re_assign_ycoord_df <- function(df, currentNode) {

+    while(any(is.na(df$y))) {

+        pNode <- with(df, parent[match(currentNode, node)]) %>% unique

+        idx <- sapply(pNode, function(i) with(df, all(node[parent == i & parent != node] %in% currentNode)))

+        newNode <- pNode[idx]

+        ## newNode <- newNode[is.na(df[match(newNode, df$node), "y"])]

+        

+        df[match(newNode, df$node), "y"] <- sapply(newNode, function(i) {

+            with(df, mean(y[parent == i], na.rm = TRUE))

+        })

+        traced_node <- as.vector(sapply(newNode, function(i) with(df, node[parent == i])))

+        currentNode <- c(currentNode[! currentNode %in% traced_node], newNode)

+    }

+    return(df)

+}

+

@@ -1,3 +1,11 @@

+get_tree_view <- function(tree_view) {

+    if (is.null(tree_view)) 

+        tree_view <- last_plot()

+

+    return(tree_view)

+}

+

+

 has.slot <- function(object, slotName) {

     if (!isS4(object)) {

         return(FALSE)

@@ -407,23 +415,6 @@ is.tree_attribute_ <- function(p, var) {

 }

-`%add%` <- function(p, data) {

-    p$data <- p$data %add2% data

-    return(p)

-}

-

-`%add2%` <- function(d1, d2) {

-    if ("node" %in% colnames(d2)) {

-        d2 <- d2[,-1] ## drop label column

-        dd <- merge(d1, d2, by.x="node", by.y="node", all.x=TRUE)

-    } else {

-        d2[,1] <- as.character(d2[,1])

-        dd <- merge(d1, d2, by.x="label", by.y=1, all.x=TRUE)

-    }

-    dd <- dd[match(d1$node, dd$node),]

-    return(dd)

-}

-

 `%place%` <- function(pg, tree) {

     param <- attr(pg, "param")

     pg$data <- fortify(tree,

deleted file mode 100644

@@ -1,13 +0,0 @@

-##' view a clade of tree

-##'

-##' 

-##' @title viewClade

-##' @param tree_view full tree view 

-##' @param node internal node number

-##' @return clade plot

-##' @export

-##' @author Guangchuang Yu

-viewClade <- function(tree_view, node) {

-    cpos <- get_clade_position(tree_view, node=node)

-    with(cpos, p+xlim(xmin, xmax*1.01)+ylim(ymin, ymax))

-}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{collapse}

 \alias{collapse}

 \title{collapse}

 \usage{

-collapse(tree_view, node)

+collapse(tree_view = NULL, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{expand}

 \alias{expand}

 \title{expand}

 \usage{

-expand(tree_view, node)

+expand(tree_view = NULL, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{flip}

 \alias{flip}

 \title{flip}

 \usage{

-flip(tree_view, node1, node2)

+flip(tree_view = NULL, node1, node2)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{get_taxa_name}

 \alias{get_taxa_name}

 \title{get_taxa_name}

 \usage{

-get_taxa_name(tree_view, node)

+get_taxa_name(tree_view = NULL, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{rotate}

 \alias{rotate}

 \title{rotate}

 \usage{

-rotate(tree_view, node)

+rotate(tree_view = NULL, node)

 }

 \arguments{

 \item{tree_view}{tree view}

@@ -1,10 +1,10 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/ggtree.R

+% Please edit documentation in R/clade-functions.R

 \name{scaleClade}

 \alias{scaleClade}

 \title{scaleClade}

 \usage{

-scaleClade(tree_view, node, scale = 1, vertical_only = TRUE)

+scaleClade(tree_view = NULL, node, scale = 1, vertical_only = TRUE)

 }

 \arguments{

 \item{tree_view}{tree view}

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

 \alias{scale_x_ggtree}

 \title{scale_x_ggtree}

 \usage{

-scale_x_ggtree(p, breaks = NULL, labels = NULL)

+scale_x_ggtree(tree_view, breaks = NULL, labels = NULL)

 }

 \arguments{

-\item{p}{tree view}

+\item{tree_view}{tree view}

 \item{breaks}{breaks for tree}

@@ -1,15 +1,17 @@

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/viewClade.R

+% Please edit documentation in R/clade-functions.R

 \name{viewClade}

 \alias{viewClade}

 \title{viewClade}

 \usage{

-viewClade(tree_view, node)

+viewClade(tree_view = NULL, node, xmax_adjust = 0)

 }

 \arguments{

 \item{tree_view}{full tree view}

 \item{node}{internal node number}

+

+\item{xmax_adjust}{adjust xmax}

 }

 \value{

 clade plot

@@ -109,6 +109,9 @@ The _`groupOTU`_ method is used for clustering related OTUs (from tips to their

 The _`fortify`_ method is used to convert tree object to a `data.frame` which is familiar by `R` users and easy to manipulate. The output `data.frame` contains tree information and all evolutionary evidences (if available, e.g. _*dN/dS*_ in `codeml` object).

+Detail descriptions of `slots` defined in each class are documented in class man pages. Users can use `class?className` (e.g. `class?beast`) to access man page of a class.

+

+

 # Getting Tree Data into R

 ## Parsing BEAST output

@@ -56,6 +56,15 @@ p <- ggtree(tree)

 MRCA(p, tip=c('A', 'E'))

 ```

+# view Clade

+

+`ggtree` provides a function `viewClade` to visualize a clade of a phylogenetic tree.

+

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

+viewClade(p+geom_tiplab(), node=21)

+```

+

+

 # group Clades

 The `ggtree` package defined several functions to manipulate tree view. _`groupClade`_ and _`groupOTU`_ methods for clustering clades or related OTUs. _`groupClade`_ accepts an internal node or a vector of internal nodes to cluster clade/clades.