@@ -6,5 +6,8 @@ Justin Silverman

 JustGitting

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

-+ `Add daylight layout for unrooted trees`

-  - <https://github.com/GuangchuangYu/ggtree/pull/124>

\ No newline at end of file

++ Annotation functions (`geom_hilight_encircle` & `geom_cladelabel2`) for

+  unrooted layout

+  - <https://github.com/GuangchuangYu/ggtree/pull/152>

++ Add daylight layout for unrooted trees

+  - <https://github.com/GuangchuangYu/ggtree/pull/124>

@@ -23,6 +23,7 @@ Imports:

     magrittr,

     methods,

     rvcheck,

+    scales,

     tidyr,

     utils

 Suggests:

@@ -33,7 +34,6 @@ Suggests:

     knitr,

     prettydoc,

     rmarkdown,

-    scales,

     testthat

 VignetteBuilder: knitr

 ByteCompile: true

@@ -92,7 +92,6 @@ export(scale_color)

 export(scale_x_ggtree)

 export(set_hilight_legend)

 export(stat_balance)

-export(stat_chull)

 export(stat_hilight)

 export(subview)

 export(theme_inset)

@@ -175,11 +174,14 @@ importFrom(graphics,identify)

 importFrom(grid,convertX)

 importFrom(grid,convertY)

 importFrom(grid,dataViewport)

+importFrom(grid,gpar)

 importFrom(grid,grid.layout)

 importFrom(grid,grid.locator)

 importFrom(grid,grid.newpage)

+importFrom(grid,grobTree)

 importFrom(grid,pushViewport)

 importFrom(grid,rasterGrob)

+importFrom(grid,rectGrob)

 importFrom(grid,unit)

 importFrom(grid,viewport)

 importFrom(magrittr,"%<>%")

@@ -189,6 +191,7 @@ importFrom(magrittr,equals)

 importFrom(methods,is)

 importFrom(methods,missingArg)

 importFrom(rvcheck,get_fun_from_pkg)

+importFrom(scales,alpha)

 importFrom(tidyr,gather)

 importFrom(treeio,as.phylo)

 importFrom(treeio,as.treedata)

@@ -1,5 +1,7 @@

 CHANGES IN VERSION 1.9.4

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

+ o geom_hilight_encircle and geom_cladelabel2 <2017-09-12, Tue>

+   + https://github.com/GuangchuangYu/ggtree/pull/152

  o set_hilight_legend <2017-08-30, Wed>

  o geom_motif for aligned motif <2017-08-22, Tue>

    + https://github.com/GuangchuangYu/ggtree/issues/148

deleted file mode 100644

@@ -1 +0,0 @@

-stat_chull.R

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

 ##' Find Most Recent Common Ancestor among a vector of tips

 ##'

-##' 

+##'

 ##' @title MRCA

 ##' @param obj supported tree object or ggplot object

 ##' @param tip a vector of mode numeric or character specifying the tips

@@ -41,16 +41,16 @@ getMRCA.df <- function(data, tip) {

 getMRCA.df_internal <- function(data, tip, anc) {

     node1 <- which(tip == data$label | tip == data[, "node"])

     node2 <- which(anc == data$label | anc == data[, "node"])

-    

+

     anc1 <- get.ancestor.df(data, node1)

     anc2 <- get.ancestor.df(data, node2)

-    

+

     if(is.null(anc1)){

       print("Warning getMRCA.df_internal(): tip is root")

-    }else if(is.null(anc1)){

+    } else if(is.null(anc2)){

       print("Warning getMRCA.df_internal(): anc is root")

     }

-    

+

     # Return common ancestors.

     intersect(c(node1, anc1), c(node2, anc2))[1]

 }

@@ -7,14 +7,14 @@

 ##' @param offset offset of bar and text from the clade

 ##' @param offset.text offset of text from bar

 ##' @param offset.bar offset of bar from text

-##' @param align logical 

+##' @param align logical

 ##' @param barsize size of bar

 ##' @param fontsize font size of text

-##' @param angle angle of text

+## @param angle angle of text

 ##' @param geom one of 'text' or 'label'

 ##' @param hjust justify text horizontally

 ##' @param color color for clade & label, of length 1 or 2

-##' @param fill fill label background, only work with geom='label'

+## @param fill fill label background, only work with geom='label'

 ##' @param family sans by default, can be any supported font

 ##' @param parse logical, whether parse label

 ##' @param ... additional parameter

@@ -33,23 +33,23 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

     na.rm <- TRUE

     inherit.aes <- FALSE

-    

+

     # create custom arguments from ellipsis (aka '...') for stat_cladeText2 depending on geom type

-    

-    # http://ggplot2.tidyverse.org/reference/geom_text.html 

+

+    # http://ggplot2.tidyverse.org/reference/geom_text.html

     # geom_label(mapping = NULL, data = NULL, stat = "identity",

     #            position = "identity", ..., parse = FALSE, nudge_x = 0, nudge_y = 0,

     #            label.padding = unit(0.25, "lines"), label.r = unit(0.15, "lines"),

     #            label.size = 0.25, na.rm = FALSE, show.legend = NA,

     #            inherit.aes = TRUE)

-    # 

+    #

     # geom_text(mapping = NULL, data = NULL, stat = "identity",

     #           position = "identity", ..., parse = FALSE, nudge_x = 0, nudge_y = 0,

     #           check_overlap = FALSE, na.rm = FALSE, show.legend = NA,

     #           inherit.aes = TRUE)

     #

     # Aesthetics: x, y, label, alpha, angle, colour, family, fontface, group, hjust, lineheight, size, vjust

-    

+

     # http://ggplot2.tidyverse.org/reference/geom_segment.html

     # geom_curve(mapping = NULL, data = NULL, stat = "identity",

     #            position = "identity", ..., curvature = 0.5, angle = 90, ncp = 5,

@@ -57,38 +57,38 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

     #            inherit.aes = TRUE)

     #

     # Aesthetics:  x, y, xend, yend, alpha, colour, group, linetype, size

-    

+

     # name_mapping = list('oldA'='newA', 'oldB'='newB')

     # data_list = list(oldB=1, oldA=2)

     # names(data_list) = name_mapping[match(names(data_list), names(name_mapping))]

-    

-    arg_list_geom_label <- c( "nudge_x", "nudge_y", "label.padding", "label.r", "label.size", 

+

+    arg_list_geom_label <- c( "nudge_x", "nudge_y", "label.padding", "label.r", "label.size",

                               "alpha", "angle", "fontface", "group", "lineheight", "size", "vjust", "fill")

-    

-    arg_list_geom_text <- c( "nudge_x", "nudge_y", "check_overlap", 

+

+    arg_list_geom_text <- c( "nudge_x", "nudge_y", "check_overlap",

                              "alpha", "angle", "fontface", "group", "lineheight", "size", "vjust")

-    

+

     # ignore angle

-    arg_list_geom_curve <- c( "curvature", "ncp", "arrow", "lineend", 

+    arg_list_geom_curve <- c( "curvature", "ncp", "arrow", "lineend",

                               "alpha", "group", "linetype")

-    

-    

+

+

     # Parse ellipsis to collect parameters for geom_text or geom_label

     ellipsis <- list(...)

     if (geom == "text") {

-      args_stat_cladeText2 <- ellipsis[names(ellipsis) %in% arg_list_geom_text]  

+      args_stat_cladeText2 <- ellipsis[names(ellipsis) %in% arg_list_geom_text]

     } else {

       args_stat_cladeText2 <- ellipsis[names(ellipsis) %in% arg_list_geom_label]

     }

-    

+

     if (parse == 'emoji') {

       emoji <- get_fun_from_pkg("emojifont", "emoji")

       label <- emoji(label)

       parse <- FALSE

       family <- "EmojiOne"

     }

-    

-    

+

+

     # add parameters to stat_cladeText2 options.

     args_stat_cladeText2$node        <- node

     args_stat_cladeText2$label       <- label

@@ -99,16 +99,16 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

     args_stat_cladeText2$family      <- family

     args_stat_cladeText2$mapping     <- mapping

     args_stat_cladeText2$data        <- data

-    args_stat_cladeText2$geom        <- geom 

+    args_stat_cladeText2$geom        <- geom

     args_stat_cladeText2$position    <- position

     args_stat_cladeText2$show.legend <- show.legend

-    args_stat_cladeText2$inherit.aes <- inherit.aes 

+    args_stat_cladeText2$inherit.aes <- inherit.aes

     args_stat_cladeText2$na.rm       <- na.rm

-    args_stat_cladeText2$parse       <- parse 

-    

+    args_stat_cladeText2$parse       <- parse

+

     # create arg list of stat_cladeBar2.

     args_stat_cladeBar2 <- ellipsis[names(ellipsis) %in% arg_list_geom_curve]

-    

+

     args_stat_cladeBar2$size        <- barsize

     args_stat_cladeBar2$node        <- node

     args_stat_cladeBar2$offset      <- offset+offset.bar

@@ -120,8 +120,8 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

     args_stat_cladeBar2$show.legend <- show.legend

     args_stat_cladeBar2$inherit.aes <- inherit.aes

     args_stat_cladeBar2$na.rm       <- na.rm

-    

-    

+

+

     if (!is.null(color)) {

         if (length(color) > 2) {

           stop("color should be of length 1 or 2")

@@ -136,7 +136,7 @@ geom_cladelabel2 <- function(node, label, offset=0, offset.text=0, offset.bar=0,

           args_stat_cladeBar2$colour <- color[2]

         }

     }

-    

+

     # print('text opts') # Debug

     # print(args_stat_cladeText2) # Debug

     # print('bar opts') # Debug

@@ -165,7 +165,7 @@ stat_cladeText2 <- function(mapping=NULL, data=NULL,

   } else {

     mapping <- modifyList(mapping, default_aes)

   }

-  

+

   layer(stat=StatCladeText2,

         data=data,

         mapping=mapping,

@@ -181,25 +181,25 @@ stat_cladeText2 <- function(mapping=NULL, data=NULL,

                     na.rm  = na.rm,

                     parse  = parse,

                     ...)

-        

+

   )

-  

+

 }

-      

+

 stat_cladeBar2 <- function(mapping=NULL, data=NULL,

                            geom="curve", position="identity",

                            node, offset, align, ...,

                            show.legend=NA, inherit.aes=FALSE, na.rm=FALSE) {

   default_aes <- aes_(x=~x, y=~y, node=~node, parent=~parent, xend=~x, yend=~y)

   if (is.null(mapping)) {

-    mapping <- default_aes 

+    mapping <- default_aes

   } else {

     mapping <- modifyList(mapping, default_aes)

   }

-  

+

   layer(stat=StatCladeBar2,

         data=data,

-        mapping=mapping, 

+        mapping=mapping,

         geom=geom,

         position=position,

         show.legend = show.legend,

@@ -210,12 +210,12 @@ stat_cladeBar2 <- function(mapping=NULL, data=NULL,

                     align=align,

                     na.rm=na.rm,

                     ...)

-        

+

   )

 }

 StatCladeText2 <- ggproto("StatCladeText2", Stat,

-                          

+

                           required_aes = c("x", "y", "label"),

                           compute_group = function(self, data, scales, params = NULL, node, label, offset, align) {

@@ -223,8 +223,8 @@ StatCladeText2 <- ggproto("StatCladeText2", Stat,

                             # computer_group does not need to return df$label as label is declared in the geom_cladelabel2() function.

                             # The data.frame returned by computer_group() does not override the variables explicitly specified in the geom_cladelabel2()

-                            # df$label <- label 

-                            

+                            # df$label <- label

+

                             if(is.null(params$angle)){

                               df$angle <- df$theta_label * 180

                               if( df$angle > 90 & df$angle < 270){

@@ -232,15 +232,15 @@ StatCladeText2 <- ggproto("StatCladeText2", Stat,

                                 df$angle <- df$angle + 180

                               }

                             }

-                          

+

                             return(df)

                           }

 )

 StatCladeBar2 <- ggproto("StatCladeBar2", Stat,

-                        

+

                         required_aes = c("x", "y", "xend", "yend"),

-                        

+

                         compute_group = function(self, data, scales, params, node, offset, align) {

                           df <- get_cladelabel2_position_bar(data, node, offset, align, adjustRatio=1.1)

                           return(df)

@@ -249,19 +249,19 @@ StatCladeBar2 <- ggproto("StatCladeBar2", Stat,

 get_cladelabel2_position_label <- function(data, node, offset, align, adjustRatio) {

   df <- get_cladelabel2_position_(data, node)

-  

+

   if (align) {

     # Find max radius from tree root.

     r <- max(getNodeEuclDistances(data, getRoot.df(data)))

   } else {

     r <- df$r

   }

-  

+

   r <- r * adjustRatio + offset

-  

+

   # Calculate the angle between theta_left and theta_right

   delta <- df$theta_left - df$theta_right

-  

+

   if(delta > 0){

     theta_label <- delta/2 + df$theta_right

   }else if(delta < 0){

@@ -270,18 +270,18 @@ get_cladelabel2_position_label <- function(data, node, offset, align, adjustRati

   }else{

     theta_label <- df$theta_left

   }

-  

+

   # correct if theta_label > 360

   if(theta_label > 2){

-    theta_label <-  theta_label - 2 

+    theta_label <-  theta_label - 2

   }

-  

+

   # Calculate the position of the label

   x1 <- r*cospi(theta_label) + data[data$node==node, 'x']

   y1 <- r*sinpi(theta_label) + data[data$node==node, 'y']

-  

+

   data.frame(x=x1, y=y1, theta_label=theta_label)

-  

+

 }

@@ -302,8 +302,8 @@ get_cladelabel2_position_bar <- function(data, node, offset, align, adjustRatio)

   y1 <- r*sinpi(df$theta_right) + data[data$node==node, 'y']

   xend <- r*cospi(df$theta_left) + data[data$node==node, 'x']

   yend <- r*sinpi(df$theta_left) + data[data$node==node, 'y']

-  

-  data.frame(x=x1, y=y1, xend=xend, yend=yend)  

+

+  data.frame(x=x1, y=y1, xend=xend, yend=yend)

 }

@@ -311,11 +311,11 @@ get_cladelabel2_position_bar <- function(data, node, offset, align, adjustRatio)

 get_cladelabel2_position_ <- function(data, node) {

   # get left and right angles of the clade subtree.

   subtree <- list( subtree = getSubtree.df(data, node), node = node )

-  

+

   arc <- getTreeArcAngles(data, node, subtree)

   # get max distance from node to clade tips.

   r <- max(getNodeEuclDistances(data[data$node %in% subtree$subtree,], node))

-  

+

   data.frame(r=r, theta_left=as.numeric(arc['left']), theta_right=as.numeric(arc['right']))

 }

@@ -1,14 +1,19 @@

-# Encircle code originally from:

-# https://github.com/hrbrmstr/ggalt/blob/master/R/geom_encircle.r

+## Encircle code originally from:

+## https://github.com/hrbrmstr/ggalt/blob/master/R/geom_encircle.r

-# draw_key_hack

+### draw_key_hack

+

+##' @importFrom scales alpha

+##' @importFrom grid grobTree

+##' @importFrom grid rectGrob

+##' @importFrom grid gpar

 draw_key_hack <- function(data, params, size) {

   print('draw_key_hack') ##DEBUG

   data$fill <- alpha(data$fill, data$alpha)

   data$alpha <- 1

-  

+

   grobTree(

-    if (!is.na(data$fill)) grid::rectGrob(gp = gpar(col = NA, fill = data$fill)),

+    if (!is.na(data$fill)) rectGrob(gp = gpar(col = NA, fill = data$fill)),

     draw_key_path(data, params)

   )

 }

@@ -35,9 +40,9 @@ GeomHilight <- ggproto("GeomHilight", Geom,

                                          size     = 1,

                                          s_shape  = 0.5,  ## corresponds to default shape in xspline of -0.5

                                          s_open   = FALSE),

-                       

+

                        draw_key = draw_key_hack, ## ???

-                       

+

                        # # Find set of nodes that define the clade.

                        # setup_params = function(data, params) {

                        #   print('setup_params()') ## DEBUG

@@ -45,80 +50,80 @@ GeomHilight <- ggproto("GeomHilight", Geom,

                        #     # Assume clade subset is given by user via data = data[subset]

                        #     return(params)

                        #   }

-                       #   

+                       #

                        #   # Find set of child nodes from clade_node.

                        #   clade_node <- 15

-                       #   

+                       #

                        #   #params$clade_root_node <- clade_node

                        #   params

                        # },

-                       

+

                        draw_group = function(data, panel_scales, coord) {

                          # Determine if tree is circular or radial as uses Polar coordinates.

                          #"CoordCartesian" %in% class(coord)

                          #"CoordPolar" %in% class(coord)

-                         

+

                          # Get clade root node and clade node ids.

                          clade_root_node <- data[1,]$clade_root_node

-                         

+

                          # Check if clade parent node exists in data.

                          if( !(clade_root_node %in% data$node) ){

                            cat('ERROR: clade node id (',clade_root_node,') not found in tree data.\n')

                            return(NULL)

                          }

-                         

+

                          clade_ids = ggtree:::getSubtree.df(data, clade_root_node)

-                         

+

                          # Remove non-clade rows.

                          data <- data[data$node %in% clade_ids,]

-                         

+

                          # # Get layout

                          #

                          # layout <- data[1,]$layout

-                         # 

+                         #

                          # If layout is {"rectangular”, “slanted”, “fan”, “circular”, “radial”} then find set of points that define

                          # the retangular region around the clade.

                          # if( layout %in% c('rectangular', 'slanted', 'fan', 'circular', 'radial') ){

-                         #   

+                         #

                          #   # get number of clade nodes.

                          #   n <- nrow(data)

-                         #   

+                         #

                          #   # Find min and max (x,y) coordinates to find rectangle covering the clade.

                          #   X <- data$x

                          #   #Y <- data$y

-                         #   

+                         #

                          #   min_x <- min(X)

                          #   max_x <- max(X)

                          #   #min_y <- min(Y)

                          #   #max_y <- max(Y)

-                         #   

-                         #   

+                         #

+                         #

                          #   # Start with single row

                          #   #data <- data[1,]

                          #   #data <- data[rep(seq_len(nrow(data)), 4), ]

                          #   #data$x <- c(max_x, min_x, min_x, max_x)

                          #   #data$y <- c(min_y, max_y, min_y, max_y)

-                         #   

+                         #

                          #   points_right <- data

                          #   # Update points with bounded box (min and max of X )

                          #   data$x <- min_x

                          #   points_right$x <- max_x

                          #   print('points_right')

                          #   print(points_right)

-                         #   

+                         #

                          #   # Combine left and right extreme points

                          #   data <- rbind(data, points_right)

-                         #   

+                         #

                          #   print('Box data') #DEBUG

                          #   print(data) #DEBUG

-                         #                             

+                         #

                          # }

-                         

+

                          # Create glob

                          glob <- get_glob_encircle(data, panel_scales, coord)

-                         

+

                          return(glob)

-                         

+

                        }

 )

@@ -127,30 +132,30 @@ get_glob_encircle <- function(data, panel_scales, coord){

   coords <- coord$transform(data, panel_scales)

   first_row <- coords[1, , drop = FALSE]

   rownames(first_row) <- NULL ## prevent warning later

-  

+

   m <- lapply(coords[,c("x","y")],mean,na.rm=TRUE)

   ch <- grDevices::chull(coords[c("x","y")])

-  

+

   mkcoords <- function(x,y) {

     data.frame(x,y,first_row[!names(first_row) %in% c("x","y")])

   }

-  

+

   coords <- coords[ch,]

   ## FIXME: using grid:: a lot. importFrom instead?

-  

+

   ## convert from lengths to physical units, for computing *directions*

   cc <- function(x,dir="x")

     grid::convertUnit(grid::unit(x,"native"),"mm",typeFrom="dimension",

                       axisFrom=dir,valueOnly=TRUE)

-  

+

   ## convert back to native (e.g. native + snpc offset)

   cc_inv <- function(x,dir="x")

     grid::convertUnit(x,"native",typeFrom="location",

                       axisFrom=dir,valueOnly=TRUE)

-  

+

   cc_comb <- function(x1,x2,dir="x")

     cc_inv(unit(x1,"native")+unit(x2,"snpc"),dir=dir)

-  

+

   ## find normalized vector: d1 and d2 have $x, $y elements

   normFun <- function(d1,d2) {

     dx <- cc(d1$x-d2$x)

@@ -158,7 +163,7 @@ get_glob_encircle <- function(data, panel_scales, coord){

     r <- sqrt(dx*dx+dy*dy)

     list(x=dx/r,y=dy/r)

   }

-  

+

   if (nrow(coords)==1) {

     ## only one point: make a diamond by spreading points vertically

     ## and horizontally

@@ -185,11 +190,11 @@ get_glob_encircle <- function(data, panel_scales, coord){

       mkcoords(x,y)

     })

   }

-  

+

   disp <- normFun(coords,m)

-  

+

   ## browser()

-  

+

   gp <- grid::get.gpar()

   pars1 <- c("colour","linetype","alpha","fill","size")

   pars2 <- c("col","lty","alpha","fill","lwd")

@@ -202,7 +207,7 @@ get_glob_encircle <- function(data, panel_scales, coord){

     shape = coords$s_shape-1,  ## kluge!

     open = first_row$s_open,

     gp = gp)

-  

+

 }

@@ -210,15 +215,18 @@ get_glob_encircle <- function(data, panel_scales, coord){

 #' layer of hilight clade with xspline

 #'

 #' @title geom_hilight_encircle

+#' @param data data frame to calculate xspline (default = NULL)

 #' @param node selected node to hilight (required)

+#' @param mapping aesthetic mapping (default = NULL)

 #' @param fill colour fill (default = steelblue)

 #' @param alpha alpha (transparency) (default = 0.5)

 #' @param expand expands the xspline clade region only (default = 0)

-#' @param spread spread of shape? (default = 0.1)

-#' @param linetype Line type of xspline (default = 1)

-#' @param size Size of xspline line (default = 1)

-#' @param s_shape Corresponds to shape of xspline (default = 0.5)  

-#' @param s_open Boolean switch determines if xspline shape is open or closed. (default = FALSE)

+#' @param ... addtional parameters, including:

+#' 'spread' spread of shape? (default = 0.1),

+#' 'linetype' Line type of xspline (default = 1),

+#' 'size' Size of xspline line (default = 1),

+#' 's_shape' Corresponds to shape of xspline (default = 0.5),

+#' 's_open' Boolean switch determines if xspline shape is open or closed. (default = FALSE)

 #' @return ggplot2

 #' @export

 #' @importFrom ggplot2 aes_

@@ -229,41 +237,41 @@ geom_hilight_encircle <- function(data = NULL,

                                   alpha       = 0.5,

                                   expand      = 0, # expand whole hilight region.

                                   ...) {

-  

+

   position    = "identity"

   na.rm       = TRUE

   show.legend = NA

   inherit.aes = FALSE

   check.aes   = FALSE

-  

-  

+

+

   # Select fields(columns) from the ggtree "data" data.frame to be passed to the GeomHilight ggproto object.

   default_aes <- aes_( x=~x, y=~y, node=~node, parent=~parent, branch.length=~branch.length )

-  

+

   if (is.null(mapping)) {

     mapping <- default_aes

   } else {

     mapping <- modifyList(mapping, default_aes)

   }

-  

+

   # create xspline geom for non-uniform trees, e.g. unrooted layout

-  l <- layer( 

+  l <- layer(

     geom = GeomHilight,

     stat = "identity",

-    mapping = mapping,  

-    data = data, 

-    position = position, 

-    show.legend = show.legend, 

+    mapping = mapping,

+    data = data,

+    position = position,

+    show.legend = show.legend,

     inherit.aes = inherit.aes,

     check.aes = check.aes,

-    params = list(clade_root_node = node, 

+    params = list(clade_root_node = node,

                   fill = fill,

                   alpha = alpha,

                   expand = expand,

                   na.rm = na.rm,

                   ...) # Parameters  to geom

   )

-  

+

   return(l)

-  

-}

\ No newline at end of file

+

+}

@@ -163,7 +163,7 @@ reroot_node_mapping <- function(tree, tree2) {

 ##' @importFrom ape reorder.phylo

 layout.unrooted <- function(tree, branch.length="branch.length", layout.method="equal_angle", ...) {

-  

+

     df <- switch(layout.method,

                  equal_angle = layoutEqualAngle(tree, branch.length),

                  daylight = layoutDaylight(tree, branch.length)

@@ -318,7 +318,7 @@ layoutDaylight <- function( tree, branch.length ){

             result <- applyLayoutDaylight(tree_df, currentNode_id)

             tree_df <- result$tree

             total_max <- total_max + result$max_change

-            

+

         }

         # Calculate the running average of angle changes.

         ave_change <- total_max / length(nodes) * length(i)

@@ -462,15 +462,15 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     # Special case.

     # get angle from parent of subtree to children

     children_ids <- getChild.df(df, subtree_root_id)

-    

+

     if(length(children_ids) == 2){

       # get angles from parent to it's two children.

       theta1 <- getNodeAngle.df(df, origin_id, children_ids[1])

       theta2 <- getNodeAngle.df(df, origin_id, children_ids[2])

-      

+

       delta <- theta1 - theta2

-      

-  

+

+

       # correct delta for points crossing 180/-180 quadrant.

       if(delta > 1){

         delta_adj = delta - 2

@@ -479,7 +479,7 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

       }else{

         delta_adj <- delta

       }

-  

+

       if(delta_adj >= 0){

         theta_left = theta1

         theta_right = theta2

@@ -492,7 +492,7 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

       theta_left <- getNodeAngle.df(df, origin_id, children_ids[1])

       theta_right <- theta_left

     }

-    

+

   }else{

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

     tree_root <- getRoot.df(df)

@@ -505,12 +505,12 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     }

   }

-  

+

   # no parent angle found.

   if (is.na(theta_left) ){

     return(0)

   }

-  

+

   # create vector with named columns

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

@@ -534,7 +534,7 @@ getTreeArcAngles <- function(df, origin_id, subtree) {

     # Get angle from origin node to parent node.

     # Skip if parent_id is a tip or parent and child node are the same.

     if(origin_id == parent_id | isTip.df(df, parent_id) ){

-      next 

+      next

     }

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

@@ -642,7 +642,7 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

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

   }

-  

+

   # Now update tip labels of rotated tree.

   # angle is in range [0, 360]

   for(node in nodes){

@@ -657,17 +657,17 @@ rotateTreePoints.df <- function(df, pivot_node, nodes, angle){

           # Update tip label angle, that is parallel to edge.

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

           if(theta_parent_child > 0 ){

-            df[node, 'angle'] <- 180 * theta_parent_child   

+            df[node, 'angle'] <- 180 * theta_parent_child

           }else if(theta_parent_child < 0 ){

             df[node, 'angle'] <- 180 * ( theta_parent_child + 2 )

           }

-          

+

         }

       }

     }

   }

-  

-  

+

+

   return(df)

 }

@@ -691,7 +691,7 @@ getNodeAngle.df <- function(df, origin_node_id, node_id){

 euc.dist <- function(x1, x2) sqrt(sum((x1 - x2) ^ 2))

-##' Get the distances from the node to all other nodes in data.frame (including itself if in df)

+## Get the distances from the node to all other nodes in data.frame (including itself if in df)

 getNodeEuclDistances <- function(df, node){

   # https://stackoverflow.com/questions/24746892/how-to-calculate-euclidian-distance-between-two-points-defined-by-matrix-contain#24747155

   dist <- NULL

@@ -831,7 +831,7 @@ getSubtreeUnrooted.df <- function(df, node){

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

-  

+

   root <- which(is.na(df$parent))

   # Check if root was found.

   if(length(root) == 0){

@@ -1009,7 +1009,7 @@ isTip <- function(tr, node) {

     return(TRUE)

   }

   return(FALSE)

-  

+

 }

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

@@ -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" />

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.8.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.9.4-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) [![total](https://img.shields.io/badge/downloads-18565/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-834/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.8.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.9.4-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) [![total](https://img.shields.io/badge/downloads-18823/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-941/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--09--04-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--09--12-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) [![Backers on Open Collective](https://opencollective.com/ggtree/backers/badge.svg)](#backers) [![Sponsors on Open Collective](https://opencollective.com/ggtree/sponsors/badge.svg)](#sponsors)

@@ -27,7 +27,7 @@ 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.

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-345-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-36-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![Altmetric](https://img.shields.io/badge/Altmetric-345-green.svg?style=flat)](https://www.altmetric.com/details/10533079) [![citation](https://img.shields.io/badge/cited%20by-39-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

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

@@ -37,7 +37,7 @@ Please cite the following article when using `ggtree`:

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-18565/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-834/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) [![total](https://img.shields.io/badge/downloads-18823/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-941/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="docs/images/dlstats.png" width="890"/>

Binary files a/docs/images/citation.png and b/docs/images/citation.png differ

Binary files a/docs/images/dlstats.png and b/docs/images/dlstats.png differ

@@ -36,10 +36,6 @@ geom_cladelabel2(node, label, offset = 0, offset.text = 0, offset.bar = 0,

 \item{parse}{logical, whether parse label}

 \item{...}{additional parameter}

-

-\item{angle}{angle of text}

-

-\item{fill}{fill label background, only work with geom='label'}

 }

 \value{

 ggplot layers

@@ -8,23 +8,24 @@ geom_hilight_encircle(data = NULL, node, mapping = NULL,

   fill = "steelblue", alpha = 0.5, expand = 0, ...)

 }

 \arguments{

+\item{data}{data frame to calculate xspline (default = NULL)}

+

 \item{node}{selected node to hilight (required)}

+\item{mapping}{aesthetic mapping (default = NULL)}

+