@@ -123,6 +123,7 @@ importFrom(ggplot2,aes_)

 importFrom(ggplot2,aes_string)

 importFrom(ggplot2,annotate)

 importFrom(ggplot2,annotation_custom)

+importFrom(ggplot2,coord_cartesian)

 importFrom(ggplot2,coord_flip)

 importFrom(ggplot2,coord_polar)

 importFrom(ggplot2,draw_key_path)

@@ -141,6 +142,7 @@ importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

 importFrom(ggplot2,ggplot)

 importFrom(ggplot2,ggplotGrob)

+importFrom(ggplot2,ggplot_build)

 importFrom(ggplot2,ggproto)

 importFrom(ggplot2,guide_legend)

 importFrom(ggplot2,guides)

@@ -1,7 +1,8 @@

 CHANGES IN VERSION 1.7.5

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

+ o improve viewClade function, use coord_cartesian instead of xlim <2016-12-28, Wed>

  o remove codes that move to treeio and now ggtree depends treeio <2016-12-20, Tue>

- 

+

 CHANGES IN VERSION 1.7.4

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

  o is.ggtree function to test whether object is produced by ggtree <2016-12-06, Tue>

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

 ##' get taxa name of a selected node

 ##'

-##' 

+##'

 ##' @title get_taxa_name

 ##' @param tree_view tree view

 ##' @param node node

@@ -9,7 +9,7 @@

 ##' @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"]

@@ -21,42 +21,48 @@ get_taxa_name <- function(tree_view=NULL, node) {

 ##' view a clade of tree

 ##'

-##' 

+##'

 ##' @title viewClade

-##' @param tree_view full tree view 

+##' @param tree_view full tree view

 ##' @param node internal node number

 ##' @param xmax_adjust adjust xmax

 ##' @return clade plot

+##' @importFrom ggplot2 ggplot_build

+##' @importFrom ggplot2 coord_cartesian

 ##' @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))

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

+

+    ## 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))

 }

+

 ##' collapse a clade

 ##'

-##' 

+##'

 ##' @title collapse

-##' @param tree_view tree view 

+##' @param tree_view tree view

 ##' @param node clade node

 ##' @return tree view

 ##' @export

 ##' @seealso expand

 ##' @author Guangchuang Yu

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

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

     tree_view %<>% get_tree_view

-    

+

     df <- tree_view$data

     if (is.na(df$x[df$node == node])) {

         warning("specific node was already collapsed...")

         return(tree_view)

     }

-    

+

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

     sp.df <- df[sp,]

     df[node, "isTip"] <- TRUE

@@ -69,15 +75,15 @@ collapse <- function(tree_view=NULL, node) {

     df[sp, "x"] <- NA

     df[sp, "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

-    

+

     tree_view$data <- df

     clade <- paste0("clade_", node)

     attr(tree_view, clade) <- sp.df

@@ -86,7 +92,7 @@ collapse <- function(tree_view=NULL, node) {

 ##' expand collased clade

 ##'

-##' 

+##'

 ##' @title expand

 ##' @param tree_view tree view

 ##' @param node clade node

@@ -96,7 +102,7 @@ collapse <- function(tree_view=NULL, node) {

 ##' @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)) {

@@ -107,7 +113,7 @@ expand <- function(tree_view=NULL, node) {

     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

@@ -123,7 +129,7 @@ expand <- function(tree_view=NULL, node) {

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

-    

+

     tree_view$data <- calculate_angle(df)

     attr(tree_view, clade) <- NULL

     tree_view

@@ -131,16 +137,16 @@ expand <- function(tree_view=NULL, node) {

 ##' rotate 180 degree of a selected branch

 ##'

-##' 

+##'

 ##' @title rotate

-##' @param tree_view tree view 

+##' @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))

@@ -168,9 +174,9 @@ rotate <- function(tree_view=NULL, node) {

 ##' flip position of two selected branches

 ##'

-##' 

+##'

 ##' @title flip

-##' @param tree_view tree view 

+##' @param tree_view tree view

 ##' @param node1 node number of branch 1

 ##' @param node2 node number of branch 2

 ##' @return ggplot2 object

@@ -178,7 +184,7 @@ rotate <- function(tree_view=NULL, node) {

 ##' @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])

@@ -220,7 +226,7 @@ flip <- function(tree_view=NULL, node1, node2) {

     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$data <- calculate_angle(tree_view$data)

     tree_view

@@ -229,7 +235,7 @@ flip <- function(tree_view=NULL, node1, node2) {

 ##' scale clade

 ##'

-##' 

+##'

 ##' @title scaleClade

 ##' @param tree_view tree view

 ##' @param node clade node

@@ -242,50 +248,50 @@ flip <- function(tree_view=NULL, node1, node2) {

 ##' @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) {

         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

     df <- reassign_y_from_node_to_root(df, node)

-    

+

     ## re-calculate branch mid position

     df <- calculate_branch_mid(df)

-    

+

     tree_view$data <- calculate_angle(df)

     tree_view

 }