@@ -191,7 +191,7 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

 ##' @inheritParams get_taxa_name

 ##' @return tree view

 ##' @export

-##' examples

+##' @examples

 ##' x <- rtree(15)

 ##' p <- ggtree(x) + geom_tiplab()

 ##' p1 <- collapse(p, 17)

@@ -300,10 +300,12 @@ rotate <- function(tree_view=NULL, node) {

 ##' @param node2 node number of clade 2. It should share a same parent node with node1

 ##' @return ggplot object

 ##' @export

+##' @examples

+##' set.seed(123)

 ##' x <- rtree(15)

 ##' p <- ggtree(x) + geom_tiplab() +

 ##'   geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

-##' flip(p, 19, 20)   ## Depends on the condition of your tree

+##' flip(p, 23, 24)   ## Depends on the condition of your tree

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

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

 ##' This function extract an ordered vector of the tips from selected clade or the whole tree

 ##' based on the ggtree() plot. 

 ##' @title get_taxa_name

-##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

+##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot object will be used.

 ##' @param node internal node number to specify a clade. If NULL, using the whole tree

 ##' @return ordered taxa name vector

 ##' @importFrom tidytree offspring

@@ -35,17 +35,22 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

 }

-##' view a clade of tree

+##' view a selected clade of tree, clade can be selected by specifying a node number or 

+##' determined by the most recent common ancestor of selected tips

 ##'

 ##'

 ##' @title viewClade

 ##' @inheritParams get_taxa_name

-##' @param xmax_adjust adjust xmax

+##' @param xmax_adjust adjust the max range of x axis

 ##' @return clade plot

 ##' @importFrom ggplot2 ggplot_build

 ##' @importFrom ggplot2 coord_cartesian

 ##' @importFrom aplot xrange

 ##' @export

+##' @examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab()

+##' viewClade(p, 18, xmax_adjust = 0.)

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

@@ -70,20 +75,26 @@ is.viewClade <- function(tree_view) {

-##' collapse a clade

+##' collapse a selected clade, which can later be expanded with the 'expand()' fuction if necessary

 ##'

 ##'

 ##' @title collapse-ggtree

 ##' @rdname collapse

 ##' @param x tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

 ##' @param node internal node number 

-##' @param mode one of 'none', 'max', 'min' and 'mixed'

-##' @param clade_name set clade name. If clade_name = NULL, do nothing

-##' @param ... additional parameters

+##' @param mode one of 'none'(default), 'max', 'min' and 'mixed'. 'none' would simply collapse the clade as 'tip' and 

+##' the rest will display a triangle, whose shape is determined by the farest/closest tip of the collapsed clade to indicate it

+##' @param clade_name set a name for the collapsed clade. If clade_name = NULL, do nothing

+##' @param ... additional parameters to set the color or transparency of the triangle

 ##' @return tree view

 ##' @method collapse ggtree

 ##' @importFrom ggplot2 geom_polygon

 ##' @export

+##' @examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab()

+##' p

+##' p1 <- collapse(p, node = 17, mode = "mixed", clade_name = "cclade", alpha = 0.8, color = "grey", fill = "light blue")

 ##' @seealso expand

 ##' @author Guangchuang Yu

 collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...) {

@@ -173,13 +184,18 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

     tree_view

 }

-##' expand collased clade

+##' expand collapsed clade

 ##'

 ##'

 ##' @title expand

 ##' @inheritParams get_taxa_name

 ##' @return tree view

 ##' @export

+##' examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab()

+##' p1 <- collapse(p, 17)

+##' expand(p1, 17)

 ##' @seealso collapse

 ##' @author Guangchuang Yu

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

@@ -230,13 +246,17 @@ expand <- function(tree_view=NULL, node) {

     return(tree_view)

 }

-##' rotate 180 degree of a selected branch

+##' rotate selected clade by 180 degree

 ##'

 ##'

 ##' @title rotate

 ##' @inheritParams get_taxa_name

 ##' @return ggplot2 object

 ##' @export

+##' @examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab()

+##' rotate(p, 17)

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

@@ -271,15 +291,19 @@ rotate <- function(tree_view=NULL, node) {

-##' flip position of two selected branches

+##' exchange the position of 2 clades

 ##'

 ##'

 ##' @title flip

 ##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

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

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

-##' @return ggplot2 object

+##' @param node1 node number of clade 1. It should share a same parent node with node2

+##' @param node2 node number of clade 2. It should share a same parent node with node1

+##' @return ggplot object

 ##' @export

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab() +

+##'   geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

+##' flip(p, 19, 20)   ## Depends on the condition of your tree

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

@@ -342,17 +366,22 @@ flip <- function(tree_view=NULL, node1, node2) {

 }

-##' scale clade

+##' zoom out/in a selected clade to emphasize or de-emphasize it

 ##'

 ##'

 ##' @title scaleClade

 ##' @inheritParams get_taxa_name

-##' @param scale scale

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

+##' @param scale the scale of the selected clade. The clade will be zoom in when scale > 1,

+##' and will be zoom out when scale < 1

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

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

-##' TRUE by default.

 ##' @return tree view

 ##' @export

+##' @examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab() +

+##'   geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

+##' scaleClade(p, 24, scale = .1)

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

@@ -431,15 +460,20 @@ reassign_y_from_node_to_root <- function(df, node) {

 }

-##' zoom selected clade of a tree

+##' zoom in on a selected clade of a tree, while showing its on the full view of tree as a seperated panel for reference

 ##'

 ##' 

 ##' @title zoomClade

 ##' @inheritParams get_taxa_name

-##' @param xexpand numeric, extend x, meaning the ratio of range of original x,

+##' @param xexpand numeric, expend the xlim of the zoom area.

 ##' default is NULL.

 ##' @return full tree with zoom in clade

 ##' @author Guangchuang Yu

+##' @examples

+##' x <- rtree(15)

+##' p <- ggtree(x) + geom_tiplab() +

+##'   geom_nodelab(aes(subset=!isTip, label=node), hjust = -.1, color = "red")

+##' zoomClade(p, 21, xexpand = .2)

 ##' @export

 zoomClade <- function(tree_view = NULL, node, xexpand=NULL) {

     p <- get_tree_view(tree_view)

@@ -120,7 +120,7 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

         df <- reassign_y_from_node_to_root(df, node)

         ## re-calculate branch mid position

-        df <- calculate_branch_mid(df)

+        df <- calculate_branch_mid(df, layout=get_layout(tree_view))

         ii <- which(!is.na(df$x))

         df$angle[ii] <- calculate_angle(df[ii,])$angle

@@ -217,7 +217,7 @@ expand <- function(tree_view=NULL, node) {

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

         ## re-calculate branch mid position

-        df <- calculate_branch_mid(df)

+        df <- calculate_branch_mid(df, layout=get_layout(tree_view))

         tree_view$data <- calculate_angle(df)

     } else {

@@ -400,7 +400,7 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     df <- reassign_y_from_node_to_root(df, node)

     ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

+    df <- calculate_branch_mid(df, layout=get_layout(tree_view))

     tree_view$data <- calculate_angle(df)

@@ -1,12 +1,18 @@

 ##' get taxa name of a selected node (or tree if node=NULL) sorted by their position in plotting

 ##'

 ##'

+##' This function extract an ordered vector of the tips from selected clade or the whole tree

+##' based on the ggtree() plot. 

 ##' @title get_taxa_name

 ##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

-##' @param node internal node number 

-##' @return taxa name vector

+##' @param node internal node number to specify a clade. If NULL, using the whole tree

+##' @return ordered taxa name vector

 ##' @importFrom tidytree offspring

 ##' @export

+##' @examples

+##' tree <- rtree(30)

+##' p <- ggtree(tree)

+##' get_taxa_name(p)

 ##' @author Guangchuang Yu

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

     tree_view %<>% get_tree_view

@@ -18,6 +24,10 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

         df <- offspring(df, node)

     }

+    ## dplyr::filter(.data$isTip) %>%

+    ##     dplyr::arrange(dplyr::desc(.data$y)) %>%

+    ##     dplyr::pull(.data$label)

+

     with(df, {

         i = order(y, decreasing=T)

         label[i][isTip[i]]

@@ -426,14 +426,20 @@ reassign_y_from_node_to_root <- function(df, node) {

 ##' 

 ##' @title zoomClade

 ##' @inheritParams get_taxa_name

+##' @param xexpand numeric, extend x, meaning the ratio of range of original x,

+##' default is NULL.

 ##' @return full tree with zoom in clade

 ##' @author Guangchuang Yu

 ##' @export

-zoomClade <- function(tree_view = NULL, node) {

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

     p <- get_tree_view(tree_view)

     sp <- offspring(p, node, self_include=TRUE)

     xr <- range(sp$x)

-    xr[2] <- xr[2] + diff(xr)/10

+    if (is.null(xexpand)){

+        xr[2] <- xr[2] + diff(xr)/10

+    }else{

+        xr[2] <- xr[2] + diff(xr)/10 + xr[2]*xexpand

+    }

     yr <- range(sp$y)

     ## nn <- sp$node

     ## p + ggforce::facet_zoom(y = node %in% nn, ylim = yr)

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

 ##'

 ##'

 ##' @title get_taxa_name

-##' @param tree_view tree view

-##' @param node node

+##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

+##' @param node internal node number 

 ##' @return taxa name vector

 ##' @importFrom tidytree offspring

 ##' @export

@@ -29,8 +29,7 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

 ##'

 ##'

 ##' @title viewClade

-##' @param tree_view full tree view

-##' @param node internal node number

+##' @inheritParams get_taxa_name

 ##' @param xmax_adjust adjust xmax

 ##' @return clade plot

 ##' @importFrom ggplot2 ggplot_build

@@ -66,8 +65,8 @@ is.viewClade <- function(tree_view) {

 ##'

 ##' @title collapse-ggtree

 ##' @rdname collapse

-##' @param x tree view

-##' @param node clade node

+##' @param x tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

+##' @param node internal node number 

 ##' @param mode one of 'none', 'max', 'min' and 'mixed'

 ##' @param clade_name set clade name. If clade_name = NULL, do nothing

 ##' @param ... additional parameters

@@ -168,8 +167,7 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

 ##'

 ##'

 ##' @title expand

-##' @param tree_view tree view

-##' @param node clade node

+##' @inheritParams get_taxa_name

 ##' @return tree view

 ##' @export

 ##' @seealso collapse

@@ -226,8 +224,7 @@ expand <- function(tree_view=NULL, node) {

 ##'

 ##'

 ##' @title rotate

-##' @param tree_view tree view

-##' @param node selected node

+##' @inheritParams get_taxa_name

 ##' @return ggplot2 object

 ##' @export

 ##' @author Guangchuang Yu

@@ -268,7 +265,7 @@ rotate <- function(tree_view=NULL, node) {

 ##'

 ##'

 ##' @title flip

-##' @param tree_view tree view

+##' @param tree_view tree view (i.e. the ggtree object). If tree_view is NULL, the last ggplot will be used.

 ##' @param node1 node number of branch 1

 ##' @param node2 node number of branch 2

 ##' @return ggplot2 object

@@ -339,8 +336,7 @@ flip <- function(tree_view=NULL, node1, node2) {

 ##'

 ##'

 ##' @title scaleClade

-##' @param tree_view tree view

-##' @param node clade node

+##' @inheritParams get_taxa_name

 ##' @param scale scale

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

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

@@ -423,3 +419,25 @@ reassign_y_from_node_to_root <- function(df, node) {

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

     return(df)

 }

+

+

+##' zoom selected clade of a tree

+##'

+##' 

+##' @title zoomClade

+##' @inheritParams get_taxa_name

+##' @return full tree with zoom in clade

+##' @author Guangchuang Yu

+##' @export

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

+    p <- get_tree_view(tree_view)

+    sp <- offspring(p, node, self_include=TRUE)

+    xr <- range(sp$x)

+    xr[2] <- xr[2] + diff(xr)/10

+    yr <- range(sp$y)

+    ## nn <- sp$node

+    ## p + ggforce::facet_zoom(y = node %in% nn, ylim = yr)

+    facet_zoom <- getFromNamespace("facet_zoom", "ggforce")

+

+    p + facet_zoom(xlim = xr, ylim=yr)

+}

@@ -35,6 +35,7 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

 ##' @return clade plot

 ##' @importFrom ggplot2 ggplot_build

 ##' @importFrom ggplot2 coord_cartesian

+##' @importFrom aplot xrange

 ##' @export

 ##' @author Guangchuang Yu

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

@@ -42,7 +42,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     ## xd <- tree_view$data$branch.length[node]/2

     cpos <- get_clade_position(tree_view, node=node)

-    xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2]

+    xmax <- xrange(tree_view)[2]

     attr(tree_view, 'viewClade') <- TRUE

     attr(tree_view, 'viewClade_node') <- node

@@ -152,7 +152,7 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

     if (mode != "none") {

         tree_view <- tree_view +

             geom_polygon(mapping = aes_(x = ~x, y = ~y),

-                         data = triangle, ...)

+                         data = triangle, inherit.aes = FALSE, ...)

     }

     clade <- paste0("collapse_clade_", node)

@@ -212,8 +212,8 @@ expand <- function(tree_view=NULL, node) {

         tree_view$data <- calculate_angle(df)

     } else {

-        tree_view$data <- dplyr::bind_rows(df, sp.df) %>%

-            dplyr::arrange(.data$node)

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

+        tree_view$data <- df

     }

     attr(tree_view, clade) <- NULL

@@ -138,8 +138,9 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

                 y = c(df$y[node], sp_coord$ymin, sp_coord$ymax)                

             )

         )

-        ## remove collapsed nodes

-        df <- dplyr::filter(df, !.data$node %in% sp.df$node)

+

+        df[sp.df$node, "x"] <- NA

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

     }

     ## set clade name

@@ -147,14 +148,18 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

         df$label[node] <- clade_name

     tree_view$data <- df

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

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

+

     if (mode != "none") {

         tree_view <- tree_view +

             geom_polygon(mapping = aes_(x = ~x, y = ~y),

                          data = triangle, ...)

     }

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

+    mode_attr <- paste0("collapse_mode_", node)

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

+    attr(tree_view, mode_attr) <- mode

+

     tree_view

 }

@@ -171,38 +176,49 @@ collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...)

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

     tree_view %<>% get_tree_view

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

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

     sp.df <- attr(tree_view, clade)

+    mode_attr <- paste0("collapse_mode_", node)

+    mode <- attr(tree_view, mode_attr)

+

     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

+    if (mode == "none") {

+        ## 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)

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

-    pp <- node

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

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

-        df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

-        pp <- df$parent[pp]

-    }

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

-    j <- tidytree::child(df, pp)$node

-    j <- j[j!=pp]

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

+        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$y[getChild.df(df, pp)])

+            df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

+            pp <- df$parent[pp]

+        }

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

+        j <- tidytree::child(df, pp)$node

+        j <- j[j!=pp]

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

+        

+        ## re-calculate branch mid position

+        df <- calculate_branch_mid(df)

-    ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

+        tree_view$data <- calculate_angle(df)

+    } else {

+        tree_view$data <- dplyr::bind_rows(df, sp.df) %>%

+            dplyr::arrange(.data$node)

+    }

-    tree_view$data <- calculate_angle(df)

     attr(tree_view, clade) <- NULL

-    tree_view

+    attr(tree_view, mode_attr) <- NULL

+    return(tree_view)

 }

 ##' rotate 180 degree of a selected branch

@@ -59,6 +59,7 @@ is.viewClade <- function(tree_view) {

+

 ##' collapse a clade

 ##'

 ##'

@@ -66,15 +67,18 @@ is.viewClade <- function(tree_view) {

 ##' @rdname collapse

 ##' @param x tree view

 ##' @param node clade node

+##' @param mode one of 'none', 'max', 'min' and 'mixed'

 ##' @param clade_name set clade name. If clade_name = NULL, do nothing

 ##' @param ... additional parameters

 ##' @return tree view

 ##' @method collapse ggtree

+##' @importFrom ggplot2 geom_polygon

 ##' @export

 ##' @seealso expand

 ##' @author Guangchuang Yu

-collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

+collapse.ggtree <- function(x=NULL, node, mode = "none", clade_name = NULL, ...) {

     tree_view <- get_tree_view(x)

+    mode <- match.arg(mode, c("none", "max", "min", "mixed"))

     df <- tree_view$data

@@ -91,24 +95,52 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

         return(tree_view)

     }

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

-    sp_y <- range(sp.df$y, na.rm=TRUE)

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

-    if (length(ii)) {

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

+    if (mode == "none") {

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

+        sp_y <- range(sp.df$y, na.rm=TRUE)

+        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.df$node, "x"] <- NA

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

+

+        df <- reassign_y_from_node_to_root(df, node)

+        

+        ## re-calculate branch mid position

+        df <- calculate_branch_mid(df)

+

+        ii <- which(!is.na(df$x))

+        df$angle[ii] <- calculate_angle(df[ii,])$angle

+    } else {

+        ## reference https://jean.manguy.eu/subtrees-as-triangles-with-ggtree/

+ 

+        sp_coord <- dplyr::summarise(sp.df[sp.df$isTip,],

+                                     xmax = max(.data$x),

+                                     xmin = min(.data$x),

+                                     ymax = max(.data$y),

+                                     ymin = min(.data$y))

+ 

+        triangle <- switch(

+            mode,

+            max = tibble::tibble(

+                x = c(df$x[node], sp_coord$xmax, sp_coord$xmax),

+                y = c(df$y[node], sp_coord$ymin, sp_coord$ymax)

+            ),

+            min = tibble::tibble(

+                x = c(df$x[node], sp_coord$xmin, sp_coord$xmin),

+                y = c(df$y[node], sp_coord$ymin, sp_coord$ymax)

+            ),

+            mixed = tibble::tibble(

+                x = c(df$x[node], sp_coord$xmin, sp_coord$xmax),

+                y = c(df$y[node], sp_coord$ymin, sp_coord$ymax)                

+            )

+        )

+        ## remove collapsed nodes

+        df <- dplyr::filter(df, !.data$node %in% sp.df$node)

     }

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

-

-    df[sp.df$node, "x"] <- NA

-    df[sp.df$node, "y"] <- NA

-

-    df <- reassign_y_from_node_to_root(df, node)

-

-    ## re-calculate branch mid position

-    df <- calculate_branch_mid(df)

-

-    ii <- which(!is.na(df$x))

-    df$angle[ii] <- calculate_angle(df[ii,])$angle

     ## set clade name

     if (!is.null(clade_name))

@@ -117,6 +149,12 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

     tree_view$data <- df

     clade <- paste0("clade_", node)

     attr(tree_view, clade) <- sp.df

+    if (mode != "none") {

+        tree_view <- tree_view +

+            geom_polygon(mapping = aes_(x = ~x, y = ~y),

+                         data = triangle, ...)

+    }

+

     tree_view

 }

@@ -86,6 +86,11 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

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

     ## sp.df <- df[sp,]

     sp.df <- offspring(df, node)

+    if (nrow(sp.df) == 0) {

+        warning("input node is a tip...")

+        return(tree_view)

+    }

+

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

     sp_y <- range(sp.df$y, na.rm=TRUE)

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

@@ -145,10 +145,12 @@ expand <- function(tree_view=NULL, node) {

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

     pp <- node

     while(any(pp != root)) {

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

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

+        df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

         pp <- df$parent[pp]

     }

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

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

+    j <- tidytree::child(df, pp)$node

     j <- j[j!=pp]

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

@@ -260,10 +262,11 @@ flip <- function(tree_view=NULL, node1, node2) {

     ## yy <- df$y[-c(sp1, sp2)]

     ## df$y[-c(sp1, sp2)] <- yy + ((min(sp2.df$y, na.rm=TRUE) - max(yy)) - (min(yy) - max(sp1.df$y, na.rm=TRUE)))/2

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

+    anc <- ancestor(df, node1)$node

     ii <- match(anc, df$node)

     df[ii, "y"] <- NA

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

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

+    currentNode <- unlist(as.vector(sapply(anc, function(.node) tidytree::child(df, .node)$node)))

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

     tree_view$data <- re_assign_ycoord_df(df, currentNode)

@@ -295,7 +298,7 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     df <- tree_view$data

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

     ## sp.df <- df[sp,]

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

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

     sp <- sp.df$node

     ## sp_nr <- nrow(sp.df)

@@ -350,10 +353,12 @@ reassign_y_from_node_to_root <- function(df, node) {

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

     pp <- df$parent[node]

     while(any(pp != root)) {

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

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

+        df[pp, "y"] <- mean(tidytree::child(df, pp)$y)

         pp <- df$parent[pp]

     }

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

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

+    j <- tidytree::child(df, pp)$node

     j <- j[j!=pp]

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

     return(df)

@@ -5,6 +5,7 @@

 ##' @param tree_view tree view

 ##' @param node node

 ##' @return taxa name vector

+##' @importFrom tidytree offspring

 ##' @export

 ##' @author Guangchuang Yu

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

@@ -12,8 +13,9 @@ get_taxa_name <- function(tree_view=NULL, node=NULL) {

     df <- tree_view$data

     if (!is.null(node)) {

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

-        df <- df[sp, ]

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

+        ## df <- df[sp, ]

+        df <- offspring(df, node)

     }

     with(df, {

@@ -81,8 +83,9 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

         return(tree_view)

     }

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

-    sp.df <- df[sp,]

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

+    ## sp.df <- df[sp,]

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

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

     sp_y <- range(sp.df$y, na.rm=TRUE)

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

@@ -91,8 +94,8 @@ collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

     }

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

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

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

+    df[sp.df$node, "x"] <- NA

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

     df <- reassign_y_from_node_to_root(df, node)

@@ -170,10 +173,15 @@ rotate <- function(tree_view=NULL, node) {

     tree_view %<>% get_tree_view

     df <- tree_view$data

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

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

+    ## sp_idx <- with(df, match(sp, node))

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

+    ## sp.df <- df[sp_idx,]

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

+    sp <- sp.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$y[ii])]

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

@@ -215,11 +223,16 @@ flip <- function(tree_view=NULL, node1, node2) {

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

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

+

+    ## sp1.df <- df[sp1,]

+    ## sp2.df <- df[sp2,]

-    sp1.df <- df[sp1,]

-    sp2.df <- df[sp2,]

+    sp1.df <- offspring(df, node1, self_include = TRUE)

+    sp2.df <- offspring(df, node2, self_include = TRUE)

+    sp1 <- sp1.df$node

+    sp2 <- sp2.df$node

     min_y1 <- min(sp1.df$y, na.rm=TRUE)

     min_y2 <- min(sp2.df$y, na.rm=TRUE)

@@ -280,9 +293,11 @@ scaleClade <- function(tree_view=NULL, node, scale=1, vertical_only=TRUE) {

     }

     df <- tree_view$data

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

-    sp.df <- df[sp,]

-

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

+    ## sp.df <- df[sp,]

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

+    sp <- sp.df$node

+    

     ## sp_nr <- nrow(sp.df)

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

@@ -40,7 +40,7 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     ## xd <- tree_view$data$branch.length[node]/2

     cpos <- get_clade_position(tree_view, node=node)

-    xmax <- ggplot_build(tree_view)$layout$panel_ranges[[1]]$x.range[2]

+    xmax <- ggplot_build(tree_view)$layout$panel_params[[1]]$x.range[2]

     attr(tree_view, 'viewClade') <- TRUE

     attr(tree_view, 'viewClade_node') <- node

@@ -46,7 +46,8 @@ viewClade <- function(tree_view=NULL, node, xmax_adjust=0) {

     attr(tree_view, 'viewClade_node') <- node

     ## tree_view+xlim(cpos$xmin, xmax + xmax_adjust) + ylim(cpos$ymin, cpos$ymax)

-    tree_view + coord_cartesian(xlim=c(cpos$xmin, xmax), ylim=c(cpos$ymin, cpos$ymax), expand=FALSE)

+    tree_view + coord_cartesian(xlim=c(cpos$xmin, xmax + xmax_adjust),

+                                ylim=c(cpos$ymin, cpos$ymax), expand=FALSE)

 }

 is.viewClade <- function(tree_view) {

@@ -63,13 +63,14 @@ is.viewClade <- function(tree_view) {

 ##' @rdname collapse

 ##' @param x tree view

 ##' @param node clade node

+##' @param clade_name set clade name. If clade_name = NULL, do nothing

 ##' @param ... additional parameters

 ##' @return tree view

 ##' @method collapse ggtree

 ##' @export

 ##' @seealso expand

 ##' @author Guangchuang Yu

-collapse.ggtree <- function(x=NULL, node, ...) {

+collapse.ggtree <- function(x=NULL, node, clade_name = NULL, ...) {

     tree_view <- get_tree_view(x)

     df <- tree_view$data

@@ -100,6 +101,10 @@ collapse.ggtree <- function(x=NULL, node, ...) {

     ii <- which(!is.na(df$x))

     df$angle[ii] <- calculate_angle(df[ii,])$angle

+    ## set clade name

+    if (!is.null(clade_name))

+        df$label[node] <- clade_name

+

     tree_view$data <- df

     clade <- paste0("clade_", node)

     attr(tree_view, clade) <- sp.df

@@ -234,11 +234,12 @@ flip <- function(tree_view=NULL, node1, node2) {

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

     sp2.df$y <- sp2.df$y + max(sp1.df$y, na.rm=TRUE) + space - min(sp2.df$y, na.rm=TRUE)

+

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

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

-    yy <- df$y[-c(sp1, sp2)]

-    df$y[-c(sp1, sp2)] <- yy + ((min(sp2.df$y, na.rm=TRUE) - max(yy)) - (min(yy) - max(sp1.df$y, na.rm=TRUE)))/2

+    ## yy <- df$y[-c(sp1, sp2)]

+    ## df$y[-c(sp1, sp2)] <- yy + ((min(sp2.df$y, na.rm=TRUE) - max(yy)) - (min(yy) - max(sp1.df$y, na.rm=TRUE)))/2

     anc <- getAncestor.df(df, node1)

     ii <- match(anc, df$node)