@@ -172,9 +172,9 @@ layout.unrooted <- function(tree, branch.length="branch.length", layout.method="

 ##' 'Equal-angle layout algorithm for unrooted trees'

 ##'

-##' @references 

+##' @references

 ##' "Inferring Phylogenies" by Joseph Felsenstein.

-##' 

+##'

 ##' @title layoutEqualAngle

 ##' @param tree phylo object

 ##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.

@@ -183,9 +183,9 @@ layoutEqualAngle <- function(tree, branch.length ){

   root <- getRoot(tree)

   # Convert Phylo tree to data.frame.

   df <- as.data.frame.phylo_(tree)

-  

+

   # NOTE: Angles (start, end, angle) are in half-rotation units (radians/pi or degrees/180)

-  

+

   # create and assign NA to the following fields.

   df$x <- NA

   df$y <- NA

@@ -198,75 +198,75 @@ layoutEqualAngle <- function(tree, branch.length ){

   df[root, "start"] <- 0 # 0-degrees

   df[root, "end"]   <- 2 # 360-degrees

   df[root, "angle"] <- 0 # Angle label.

-  

+

   N <- getNodeNum(tree)

   # Get number of tips for each node in tree.

   nb.sp <- sapply(1:N, function(i) length(get.offspring.tip(tree, i)))

   # Get list of node id's.

   nodes <- getNodes_by_postorder(tree)

-  

-  for(curNode in nodes) { 

+

+  for(curNode in nodes) {

     # Get number of tips for current node.

     curNtip <- nb.sp[curNode]

     # Get array of child node indexes of current node.

     children <- getChild(tree, curNode)

-    

+

     # Get "start" and "end" angles of a segment for current node in the data.frame.

     start <- df[curNode, "start"]

     end <- df[curNode, "end"]

-    

+

     if (length(children) == 0) {

       ## is a tip

       next

     }

-    

+

     for (i in seq_along(children)) {

       child <- children[i]

       # Get the number of tips for child node.

-      ntip.child <- nb.sp[child] 

-      

+      ntip.child <- nb.sp[child]

+

       # Calculated in half radians.

       # alpha: angle of segment for i-th child with ntips_ij tips.

       # alpha = (left_angle - right_angle) * (ntips_ij)/(ntips_current)

       alpha <- (end - start) * ntip.child / curNtip

       # beta = angle of line from parent node to i-th child.

       beta <- start + alpha / 2

-      

+

       if (branch.length == "none") {

         length.child <- 1

       } else {

         length.child <- df[child, "length"]

       }

-      

+

       # update geometry of data.frame.

       # Calculate (x,y) position of the i-th child node from current node.

       df[child, "x"] <- df[curNode, "x"] + cospi(beta) * length.child

       df[child, "y"] <- df[curNode, "y"] + sinpi(beta) * length.child

-      # Calculate orthogonal angle to beta. 

+      # Calculate orthogonal angle to beta.

       df[child, "angle"] <- -90 - 180 * beta * sign(beta - 1)

       # Update the start and end angles of the childs segment.

       df[child, "start"] <- start

       df[child, "end"] <- start + alpha

       start <- start + alpha

-    } 

+    }

   }

-  

+

   return(df)

-  

+

 }

 ##' Equal daylight layout method for unrooted trees.

-##' 

+##'

 ##' #' @title

 ##' @param tree phylo object

 ##' @param branch.length set to 'none' for edge length of 1. Otherwise the phylogenetic tree edge length is used.

 ##' @return tree as data.frame with equal angle layout.

-##' @references 

+##' @references

 ##' The following aglorithm aims to implement the vague description of the "Equal-daylight Algorithm"

 ##' in "Inferring Phylogenies" pp 582-584 by Joseph Felsenstein.

-##' 

+##'

 ##' ```

 ##' Leafs are subtrees with no children

 ##' Initialise tree using equal angle algorithm

@@ -274,14 +274,14 @@ layoutEqualAngle <- function(tree, branch.length ){

 ##'

 ##' nodes = get list of nodes in tree_df breadth-first

 ##' nodes = remove tip nodes.

-##' 

+##'

 ##' ```

 layoutDaylight <- function( tree, branch.length ){

   # How to set optimal

   MAX_COUNT <- 100

   MINIMUM_AVERAGE_ANGLE_CHANGE <- 0.01

-  

+

   # Initialize tree.

   tree_df <- layoutEqualAngle(tree, branch.length)

@@ -290,16 +290,16 @@ layoutDaylight <- function( tree, branch.length ){

   # Get list of node id's.

   #nodes <- getNodes_by_postorder(tree)

   # nodes <- GetSubtree.df(tree_df, root)

-  

+

   # Get list of internal nodes

   #nodes <- tree_df[tree_df$IsTip != TRUE]$nodes

-  

+

   nodes <- getNodesBreadthFirst.df(tree_df)

   # select only internal nodes

   internal_nodes <- tree_df[!tree_df$isTip,]$node

   # Remove tips from nodes list, but keeping order.

   nodes <- intersect(nodes, internal_nodes)

-  

+

   i <- 1

   ave_change <- 1.0

   while( i <= MAX_COUNT & ave_change > MINIMUM_AVERAGE_ANGLE_CHANGE ){

@@ -307,75 +307,75 @@ layoutDaylight <- function( tree, branch.length ){

     # Reset max_change after iterating over tree.

     total_max <- 0.0

-    

+

     # for node in nodes {

     for( j in seq_along(nodes)){

       currentNode_id <- nodes[j]

-      

+

       result <- applyLayoutDaylight(tree_df, currentNode_id)

       tree_df <- result$tree

       total_max <- total_max + result$max_change

-      

+

     }

-    

+

     ave_change <- total_max / length(nodes)

-    

+

     cat('Average angle change', ave_change,'\n')

-    

+

     i <- i + 1

   }

-  

+

   return(tree_df)

-  

+

 }

 ##' Apply the daylight alorithm to adjust the spacing between the subtrees and tips of the

 ##' specified node.

-##' 

+##'

 ##' @title applyLayoutDaylight

 ##' @param df tree data.frame

 ##' @param node_id is id of the node from which daylight is measured to the other subtrees.

-##' @return list with tree data.frame with updated layout using daylight algorithm and max_change angle .

-##' 

-##'

-##' ```

-##' for node in nodes {

-##'   if node is a leaf {

-##'     next

-##'   }

-##'   

-##'   subtrees = get subtrees of node

-##'   

-##'   for i-th subtree in subtrees {

-##'     [end, start] = get left and right angles of tree from node id.

-##'     angle_list[i, 'left'] = end

-##'     angle_list[i, 'beta'] = start - end  # subtree arc angle

-##'     angle_list[i, 'index'] = i-th # index of subtree/leaf 

-##'   }

-##'

-##'   sort angle_list by 'left' column in ascending order.

-##'

-##'   D = 360 - sum( angle_list['beta'] ) # total daylight angle

-##'   d = D / |subtrees| # equal daylight angle.

-##' 

-##'   new_L = left angle of first subtree.

-##'

-##'   for n-th row in angle_list{

-##'     # Calculate angle to rotate subtree/leaf to create correct daylight angle.

-##'     new_left_angle = new_left_angle + d + angle_list[n, 'beta']

-##'     Calculate the difference between the old and new left angles.

-##'     adjust_angle = new_left_angle - angle_list[n, 'left'] 

-##'     

-##'     index = angle_list['index']

-##'     rotate subtree[index] wrt n-th node by adjust_angle

-##'     }

-##'   }

-##' }

-##' ```

+##' @return list with tree data.frame with updated layout using daylight algorithm and max_change angle.

+##

+##

+## ```

+## for node in nodes {

+##   if node is a leaf {

+##     next

+##   }

+##

+##   subtrees = get subtrees of node

+##

+##   for i-th subtree in subtrees {

+##     [end, start] = get left and right angles of tree from node id.

+##     angle_list[i, 'left'] = end

+##     angle_list[i, 'beta'] = start - end  # subtree arc angle

+##     angle_list[i, 'index'] = i-th # index of subtree/leaf

+##   }

+##

+##   sort angle_list by 'left' column in ascending order.

+##

+##   D = 360 - sum( angle_list['beta'] ) # total daylight angle

+##   d = D / |subtrees| # equal daylight angle.

+##

+##   new_L = left angle of first subtree.

+##

+##   for n-th row in angle_list{

+##     # Calculate angle to rotate subtree/leaf to create correct daylight angle.

+##     new_left_angle = new_left_angle + d + angle_list[n, 'beta']

+##     Calculate the difference between the old and new left angles.

+##     adjust_angle = new_left_angle - angle_list[n, 'left']

+##

+##     index = angle_list['index']

+##     rotate subtree[index] wrt n-th node by adjust_angle

+##     }

+##   }

+## }

+## ```

 applyLayoutDaylight <- function(df, node_id ){

-  

+

   max_change <- 0.0

-  

+

   # Get lists of node ids for each subtree, including  rest of unrooted tree.

   subtrees <- getSubtreeUnrooted.df(df, node_id)

   angle_list <- data.frame(left=numeric(0), beta=numeric(0), subtree_id=integer(0) )

@@ -384,14 +384,14 @@ applyLayoutDaylight <- function(df, node_id ){

   if(length(subtrees) <= 2){

     return( list(tree = df, max_change = max_change) )

   }

-  

+

   # Find start and end angles for each subtree.

   #   subtrees = get subtrees of node

   #   for i-th subtree in subtrees {

   for (i in seq_along(subtrees) ) {

     subtree <- subtrees[[i]]

     # [end, start] = get start and end angles of tree.

-    

+

     angles <- getTreeArcAngles(df, node_id, subtree)

     angle_list[ i, 'subtree_id'] <- i

     angle_list[ i, 'left'] <- angles['left']

@@ -399,15 +399,15 @@ applyLayoutDaylight <- function(df, node_id ){

     # If subtree arc angle is -ve, then + 2 (360).

     if(angle_list[ i, 'beta'] < 0 ){

       angle_list[ i, 'beta'] <- angle_list[ i, 'beta'] + 2

-    } 

+    }

   }

   #   sort angle_list by 'left angle' column in ascending order.

   angle_list <- angle_list[with(angle_list, order(left)), ]

   #   D = 360 - sum( angle_list['beta'] ) # total day

   #   d = D / |subtrees| # equal daylight angle.

-  total_daylight <- 2 - colSums(angle_list['beta']) 

+  total_daylight <- 2 - colSums(angle_list['beta'])

   d <- total_daylight / length(subtrees)

-   

+

   # Initialise new left-angle as first subtree left-angle.

   new_left_angle <- angle_list[1, 'left']

@@ -419,25 +419,25 @@ applyLayoutDaylight <- function(df, node_id ){

     new_left_angle <- new_left_angle + d + angle_list[i, 'beta']

     # Calculate the difference between the old and new left angles.

     adjust_angle <- new_left_angle - angle_list[i, 'left']

-    

+

     max_change <- max(max_change, abs(adjust_angle))

     #cat('Adjust angle:', abs(adjust_angle), ' Max change:', max_change ,'\n')

-    

+

     # rotate subtree[index] wrt current node

     subtree_id <- angle_list[i, 'subtree_id']

     subtree_nodes <- subtrees[[subtree_id]]$subtree

     # update tree_df for all subtrees with rotated points.

     df <- rotateTreePoints.df(df, node_id, subtree_nodes, adjust_angle)

   }

-  

-  return( list(tree = df, max_change = max_change) ) 

-  

+

+  return( list(tree = df, max_change = max_change) )

+

 }

-##' Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and 

+##' Find the right (clockwise rotation, angle from +ve x-axis to furthest subtree nodes) and

 ##' left (anti-clockwise angle from +ve x-axis to subtree)

-##' 

+##'

 ##' @title getTreeArcAngles

 ##' @param df tree data.frame

 ##' @param origin_id node id from which to calculate left and right hand angles of subtree.

@@ -448,7 +448,7 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

   theta_child <- 0.0

   subtree_root_id <- subtree$node

   subtree_node_ids <- subtree$subtree

-  

+

   # Initialise angle from origin node to parent node.

   # If subtree_root_id is child of origin_id

   if( any(subtree_root_id == getChild.df(df, origin_id)) ){

@@ -457,22 +457,22 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     # get the real root of df tree to initialise left and right angles.

     theta_parent <- getNodeAngle.df(df, origin_id, getRoot.df(df))

   }

-    

+

   # create vector with named columns

   # left-hand and right-hand angles between origin node and the extremities of the tree nodes.

   arc <- c('left' = theta_parent, 'right' = theta_parent)

-    

+

   # Subtree has to have 1 or more nodes to compare.

   if (length(subtree_node_ids) == 0 ){

     return(0)

-  } 

+  }

+

-  

   # Remove tips from nodes list, but keeping order.

   # internal_nodes <- df[!df$isTip,]$node

   # subtree_node_ids <- intersect(subtree_node_ids, internal_nodes)

-  

-  

+

+

   # Calculate the angle from the origin node to each child node.

   # Moving from parent to children in depth-first traversal.

   for( i in seq_along(subtree_node_ids) ){

@@ -482,9 +482,9 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     if(isTip.df(df, parent_id) ){ next }

     theta_parent <- getNodeAngle.df(df, origin_id, parent_id)

-  

+

     children_ids <- getChild.df(df, parent_id)

-    

+

     for( j in seq_along(children_ids)){

       #delta_x <- df[subtree_node_id, 'x'] - df[origin_id, 'x']

       #delta_y <- df[subtree_node_id, 'y'] - df[origin_id, 'y']

@@ -494,7 +494,7 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

       if( child_id == origin_id ){

         next

       }

-      

+

       theta_child <- getNodeAngle.df(df, origin_id, child_id)

       # Skip if child node is already inside arc.

@@ -505,8 +505,8 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

         # child node inside arc.

         next

       }

-      

-      

+

+

       delta <- theta_child - theta_parent

       delta_adj <- delta

       # Correct the delta if parent and child angles cross the 180/-180 half of circle.

@@ -517,12 +517,12 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

       }else if( delta < -1){ # Edge between parent and child cross upper and lower quadrants of cirlce

         delta_adj <- delta + 2 # delta' = delta - 360

       }

-      

+

       theta_child_adj <- theta_child

       # If angle change from parent to node is positive (anti-clockwise), check left angle

       if(delta_adj > 0){

-        # If child/parent edges cross the -180/180 quadrant (angle between them is > 180), 

+        # If child/parent edges cross the -180/180 quadrant (angle between them is > 180),

         # check if right angle and child angle are different signs and adjust if needed.

         if( abs(delta) > 1){

           if( arc['left'] > 0 & theta_child < 0){

@@ -531,14 +531,14 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

             theta_child_adj <- theta_child - 2

           }

         }

-        

+

           # check if left angle of arc is less than angle of child. Update if true.

         if( arc['left'] < theta_child_adj ){

           arc['left'] <- theta_child

         }

-      # If angle change from parent to node is negative (clockwise), check right angle  

+      # If angle change from parent to node is negative (clockwise), check right angle

       }else if(delta_adj < 0){

-        # If child/parent edges cross the -180/180 quadrant (angle between them is > 180), 

+        # If child/parent edges cross the -180/180 quadrant (angle between them is > 180),

         # check if right angle and child angle are different signs and adjust if needed.

         if( abs(delta) > 1){

           # Else change in angle from parent to child is negative, then adjust child angle if right angle is a different sign.

@@ -551,20 +551,20 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

         # check if right angle of arc is greater than angle of child. Update if true.

         if( arc['right'] > theta_child_adj  ){

           arc['right'] <- theta_child

-        }  

-        

+        }

+

       }

     }

-  } 

+  }

   # Convert arc angles of [1, -1] to [2,0] domain.

   arc[arc<0] <- arc[arc<0] + 2

   return(arc)

-  

+

 }

 ##' Rotate the points in a tree data.frame around a pivot node by the angle specified.

-##' 

+##'

 ##' @title rotateTreePoints.data.fram

 ##' @param df tree data.frame

 ##' @param pivot_node is the id of the pivot node.

@@ -575,7 +575,7 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

   # Rotate nodes around pivot_node.

   # x' = cos(angle)*delta_x - sin(angle)*delta_y + delta_x

   # y' = sin(angle)*delta_x + cos(angle)*delta_y + delta_y

-  

+

   cospitheta <- cospi(angle)

   sinpitheta <- sinpi(angle)

   for(node in nodes){

@@ -584,7 +584,7 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

     delta_y <- df[node, 'y'] - df[pivot_node, 'y']

     df[node, 'x'] <- cospitheta * delta_x - sinpitheta * delta_y + df[pivot_node, 'x']

     df[node, 'y'] <- sinpitheta * delta_x + cospitheta * delta_y + df[pivot_node, 'y']

-    

+

     # Update label angle if not root node.

     # get parent

     parent_id <- getParent.df(df, node)

@@ -596,13 +596,13 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

         df[node, 'angle'] <- -90 - 180 * theta_parent_child * sign(theta_parent_child - 1)

       }

     }

-    

+

   }

   return(df)

 }

 ##' Get the angle between the two nodes specified.

-##' 

+##'

 ##' @title getNodeAngle.df

 ##' @param df tree data.frame

 ##' @param origin_node_id origin node id number

@@ -622,13 +622,13 @@ getNodeAngle.df <- function(df, origin_node_id, node_id){

 ##' Get all children of node from tree, including start_node.

-##' 

+##'

 ##' @title getSubtree

 ##' @param tree ape phylo tree object

 ##' @param node is the tree node id from which the tree is derived.

 ##' @return list of all child node id's from starting node.

 getSubtree <- function(tree, node){

-  

+

   subtree <- c(node)

   i <- 1

   while( i <= length(subtree)){

@@ -640,13 +640,12 @@ getSubtree <- function(tree, node){

   return(subtree)

 }

-# Get all children of node from df tree using breath-first.

-#

+##' Get all children of node from df tree using breath-first.

+##'

 ##' @title GetSubtree.df

 ##' @param df tree data.frame

 ##' @param node id of starting node.

 ##' @return list of all child node id's from starting node.

-##' @examples

 GetSubtree.df <- function(df, node){

   subtree <- c(node)

   i <- 1

@@ -659,9 +658,9 @@ GetSubtree.df <- function(df, node){

   return(subtree)

 }

-##' Get all subtrees of specified node. This includes all ancestors and relatives of node and 

+##' Get all subtrees of specified node. This includes all ancestors and relatives of node and

 ##' return named list of subtrees.

-##' 

+##'

 ##' @title GetSubtreeUnrooted

 ##' @param tree ape phylo tree object

 ##' @param node is the tree node id from which the subtrees are derived.

@@ -672,17 +671,17 @@ GetSubtreeUnrooted <- function(tree, node){

     # return NA

     return(NA)

   }

-  

+

   subtrees <- list()

-  

+

   # get subtree for each child node.

   children_ids <- getChild(tree, node)

-  

+

   remaining_nodes <- getNodes_by_postorder(tree)

   # Remove current node from remaining_nodes list.

   remaining_nodes <- setdiff(remaining_nodes, node)

-  

-  

+

+

   for( child in children_ids ){

     # Append subtree nodes to list if not 0 (root).

     subtree <- getSubtree(tree, child)

@@ -690,7 +689,7 @@ GetSubtreeUnrooted <- function(tree, node){

     # remove subtree nodes from remaining nodes.

     remaining_nodes <- setdiff(remaining_nodes, as.integer(unlist(subtrees[[length(subtrees)]]['subtree']) ))

   }

-  

+

   # The remaining nodes that are not found in the child subtrees are the remaining subtree nodes.

   # ie, parent node and all other nodes. We don't care how they are connect, just their ids.

   parent_id <- getParent(tree, node)

@@ -698,7 +697,7 @@ GetSubtreeUnrooted <- function(tree, node){

   if( parent_id != 0 & length(remaining_nodes) >= 1){

     subtrees[[length(subtrees)+1]] <- list( node = parent_id, subtree = remaining_nodes)

   }

-  

+

   return(subtrees)

 }

@@ -714,18 +713,18 @@ getSubtreeUnrooted.df <- function(df, node){

   if( isTip.df(df, node) ){

     return(NA)

   }

-  

+

   subtrees <- list()

-  

+

   # get subtree for each child node.

   children_ids <- getChild.df(df, node)

-  

+

   # remaining_nodes <- getNodes_by_postorder(tree)

   remaining_nodes <- df$node

-  

+

   # Remove current node from remaining_nodes list.

   remaining_nodes <- setdiff(remaining_nodes, node)

-  

+

   for( child in children_ids ){

     subtree <- GetSubtree.df(df, child)

     # Append subtree nodes to list if more than 1 node in subtree (i.e. not a tip)

@@ -738,7 +737,7 @@ getSubtreeUnrooted.df <- function(df, node){

     #  remaining_nodes <- setdiff(remaining_nodes, subtree)

     #}

   }

-  

+

   # The remaining nodes that are not found in the child subtrees are the remaining subtree nodes.

   # ie, parent node and all other nodes. We don't care how they are connected, just their id.

   parent_id <- getParent.df(df, node)

@@ -746,7 +745,7 @@ getSubtreeUnrooted.df <- function(df, node){

   if( parent_id != 0 & length(remaining_nodes) >= 1){

     subtrees[[length(subtrees)+1]] <- list( node = parent_id, subtree = remaining_nodes)

   }

-  

+

   return(subtrees)

 }

@@ -1032,7 +1031,7 @@ getNodes_by_postorder <- function(tree) {

 #}

 ##' Get the nodes of tree from root in breadth-first order.

-##' 

+##'

 ##' @title getNodesBreadthFirst.df

 ##' @param df tree data.frame

 ##' @return list of node id's in breadth-first order.

@@ -1046,27 +1045,27 @@ getNodesBreadthFirst.df <- function(df){

   tree_size <- nrow(df)

   # initialise list of nodes

   res <- root

-  

+

   i <- 1

   while(length(res) < tree_size){

     parent <- res[i]

     i <- i + 1

-    

+

     # Skip if parent is a tip.

     if(isTip.df(df, parent)){

       next

     }

-    

+

     # get children of current parent.

     children <- getChild.df(df,parent)

     # add children to result

     res <- c(res, children)

-    

+

   }

-  

+

   return(res)

-  

+

 }

@@ -1426,7 +1425,7 @@ add_angle_slanted <- function(res) {

     theta <- atan(dy/dx)

     theta[is.na(theta)] <- 0 ## root node

     res$angle <- theta/pi * 180

-    

+

     branch.y <- (res[res$parent, "y"] + res[, "y"])/2

     idx <- is.na(branch.y)

     branch.y[idx] <- res[idx, "y"]

@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-13681/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/release%20version-1.6.11-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![](https://img.shields.io/badge/devel%20version-1.7.10-green.svg?style=flat)](https://github.com/guangchuangyu/ggtree) [![Bioc](http://www.bioconductor.org/shields/years-in-bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [![](https://img.shields.io/badge/download-13972/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

-[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--03-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![Project Status: Active - The project has reached a stable, usable state and is being actively developed.](http://www.repostatus.org/badges/latest/active.svg)](http://www.repostatus.org/#active) [![codecov](https://codecov.io/gh/GuangchuangYu/ggtree/branch/master/graph/badge.svg)](https://codecov.io/gh/GuangchuangYu/ggtree) [![Last-changedate](https://img.shields.io/badge/last%20change-2017--04--11-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![GitHub forks](https://img.shields.io/github/forks/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/network) [![GitHub stars](https://img.shields.io/github/stars/GuangchuangYu/ggtree.svg)](https://github.com/GuangchuangYu/ggtree/stargazers) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

 [![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![Build Status](http://www.bioconductor.org/shields/build/devel/bioc/ggtree.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [![Linux/Mac Travis Build Status](https://img.shields.io/travis/GuangchuangYu/ggtree/master.svg?label=Mac%20OSX%20%26%20Linux)](https://travis-ci.org/GuangchuangYu/ggtree) [![AppVeyor Build Status](https://img.shields.io/appveyor/ci/Guangchuangyu/ggtree/master.svg?label=Windows)](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

@@ -20,7 +20,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. 2017, 8(1):28-36.

-[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-12-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-14-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![](https://img.shields.io/badge/Altmetric-349-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -33,15 +33,15 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 ### Citation

-[![citation](https://img.shields.io/badge/cited%20by-12-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+[![citation](https://img.shields.io/badge/cited%20by-14-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

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 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-13681/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-967/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-13972/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![](https://img.shields.io/badge/download-1385/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

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

+        2015               2015.5              2016               2016.5              2017

@@ -220,7 +220,7 @@

 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

 <p><a href="https://github.com/GuangchuangYu/featured_img">Let us know</a> if you have

 published using <code>ggtree</code> and your publication will be featured here.</p>

-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-11-blue.svg?style=flat" /></a>

+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-14-blue.svg?style=flat" /></a>

 <link rel='stylesheet' href=https://guangchuangyu.github.io/resume/css/morris.css>

 <script src='https://guangchuangyu.github.io/resume/css/jquery.min.js' type='text/javascript'></script>

 <script src='https://guangchuangyu.github.io/resume/css/raphael-min.js' type='text/javascript'></script>

@@ -234,12 +234,12 @@ published using <code>ggtree</code> and your publication will be featured here.<

     height: 300px;

   }<br />

   </style>

-<div id="chart8461435aeb07" class="rChart morris"></p>

+<div id="chart8dd434d08fe" class="rChart morris"></p>

 </div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart8461435aeb07",

+ "element": "chart8dd434d08fe",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -254,11 +254,11 @@ published using <code>ggtree</code> and your publication will be featured here.<

 },

 {

  "year": 2017,

-"cites":             10,

+"cites":             13,

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart8461435aeb07",

+"id": "chart8dd434d08fe",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -218,7 +218,7 @@

 <!-- AddToAny END -->

 <p><link rel="stylesheet" href="https://guangchuangyu.github.io/css/font-awesome.min.css"></p>

-<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-11-blue.svg?style=flat" /></a></p>

+<p><a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-14-blue.svg?style=flat" /></a></p>

 <!-- citation:=HtEfBTGE9r8C:=7268358477862164627 -->

 <h2 id="journal-articles"><i class="fa fa-mortar-board"></i> Journal Articles</h2>

@@ -234,8 +234,8 @@

 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>

 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.6.11-blue.svg?style=flat" /></a>

 <a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.7.10-blue.svg?style=flat" /></a>

-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-13085/total-blue.svg?style=flat" /></a>

-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-967/month-blue.svg?style=flat" /></a></p>

+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-13972/total-blue.svg?style=flat" /></a>

+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1385/month-blue.svg?style=flat" /></a></p>

 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on

 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>

 is designed for not only viewing phylogenetic tree but also displaying

@@ -256,8 +256,8 @@ University of Hong Kong.</p>

 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>

 <p>Please cite the following article when using <code>ggtree</code>:</p>

 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>

-<a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-11-blue.svg?style=flat" /></a>

-<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-348-blue.svg?style=flat" /></a></p>

+<a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-14-blue.svg?style=flat" /></a>

+<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-349-blue.svg?style=flat" /></a></p>

 <p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R

 package for visualization and annotation of phylogenetic trees with

 their covariates and other associated data. <strong><em>Methods in Ecology and

@@ -217,7 +217,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart8461435aeb07\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             10,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart8461435aeb07\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016,82(22):6788-6798.", 

+            "text": "Let us know\n if you have\npublished using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart8dd434d08fe\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n},\n{\n \"year\": 2017,\n\"cites\":             13,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart8dd434d08fe\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016,82(22):6788-6798.", 

             "title": "Featured Articles"

         }, 

         {

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

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/</loc>

-     <lastmod>2017-03-21</lastmod>

+     <lastmod>2017-04-11</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -12,7 +12,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>

-     <lastmod>2017-03-21</lastmod>

+     <lastmod>2017-04-11</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -20,7 +20,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>

-     <lastmod>2017-03-21</lastmod>

+     <lastmod>2017-04-11</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -28,7 +28,7 @@