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

 # ggtree 1.99.1

++ bug fixed of `geom_hilight` for `tree$edge.length = NULL` (2019-10-16, Wed)

+  - <https://groups.google.com/d/msg/bioc-ggtree/GULj-eoAluI/Llpm-HbfCwAJ>

 + `fortify` method for igraph (only work with tree graph) (2019-09-28, Sat)

 + `ggdensitree` (2019-09-11, Wed)

   - <https://github.com/YuLab-SMU/ggtree/pull/253>

@@ -24,7 +24,8 @@ geom_hilight <- function(node, fill="steelblue", alpha=.5, extend=0, ...) {

-geom_hilight_rectangular <- function(node, fill="steelblue", alpha=.5, extend=0, extendto=NULL) {

+geom_hilight_rectangular <- function(node, mapping = NULL, fill="steelblue",

+                                     alpha=.5, extend=0, extendto=NULL) {

   data = NULL

   stat = "hilight"

   position = "identity"

@@ -33,8 +34,14 @@ geom_hilight_rectangular <- function(node, fill="steelblue", alpha=.5, extend=0,

   inherit.aes = FALSE

   check.aes = FALSE

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

-  mapping <- default_aes

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

+

+  if (is.null(mapping)) {

+      mapping <- default_aes

+  } else {

+      mapping <- modifyList(default_aes, mapping)

+  }

+

   layer(

     stat=StatHilight,

@@ -78,12 +85,12 @@ stat_hilight <- function(mapping=NULL, data=NULL, geom="rect",

                          fill, alpha, extend=0, extendto=NULL,

                          ...) {

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

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

   if (is.null(mapping)) {

     mapping <- default_aes

   } else {

-    mapping <- modifyList(mapping, default_aes)

+    mapping <- modifyList(default_aes, mapping)

   }

   layer(

@@ -122,7 +129,7 @@ StatHilight <- ggproto("StatHilight", Stat,

                            }

                            return(df)

                        },

-                       required_aes = c("x", "y", "branch.length")

+                       required_aes = c("x", "y") #, "branch.length")

                        )

@@ -140,7 +147,6 @@ get_clade_position <- function(treeview, node) {

 }

 get_clade_position_ <- function(data, node) {

-    #sp <- tryCatch(tidytree:::offspring.tbl_tree(data, node)$node, error=function(e) NULL)

     sp <- tryCatch(offspring.tbl_tree(data, node)$node, error=function(e) NULL)

     i <- match(node, data$node)

     if (is.null(sp)) {

@@ -155,7 +161,7 @@ get_clade_position_ <- function(data, node) {

     y <- sp.df$y

     if ("branch.length" %in% colnames(data)) {

-        xmin <- min(x, na.rm=TRUE)-data[["branch.length"]][i]/2

+        xmin <- min(x, na.rm=TRUE) - data[["branch.length"]][i]/2

     } else {

         xmin <- min(sp.df$branch, na.rm=TRUE)

     }

@@ -245,12 +245,12 @@ geom_hilight_encircle <- function(data = NULL,

   # 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 )

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

   if (is.null(mapping)) {

     mapping <- default_aes

   } else {

-    mapping <- modifyList(mapping, default_aes)

+    mapping <- modifyList(default_aes, mapping)

   }

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

@@ -123,6 +123,10 @@ ggplot_add.hilight <- function(object, plot, object_name) {

     ## instead of the tree layout, you may get graphics::layout

     if (!is.character(layout)) layout <- 'rectangular'

+    if ("branch.length" %in% colnames(plot$data)) {

+        object$mapping <- aes_(branch.length = ~branch.length)

+    }

+

     if (layout == "unrooted" || layout == "daylight") {

         ly <- do.call(geom_hilight_encircle, object)

     } else {