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

 # ggtree 1.13.1.9002

++ `extend` parameter in `geom_cladelabel` and `geom_strip` supports specifying

+  extension of both sides (2018-07-06, Fri)

 + `geom_nodelab2` for circular layout (2018-07-03, Tue)

   - <https://groups.google.com/d/msgid/bioc-ggtree/cbe5e1e3-99c4-481d-8523-d5b50cf0460b%40googlegroups.com>

 + re-export `ggplot2::fortify`

@@ -21,7 +21,7 @@ facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {

 add_panel <- function(p, panel) {

     df <- p$data

     if (is.null(df$.panel)) {

-        df$.panel <- factor("Tree")

+        df[[".panel"]] <- factor("Tree")

     }

     levels(df$.panel) %<>% c(., panel)

     p$data <- df

@@ -232,6 +232,9 @@ get_cladelabel_position <- function(data, node, offset, align, adjustRatio, angl

 # get x, y and yend of clade region.

 get_cladelabel_position_ <- function(data, node, angle = "auto", extend = 0) {

+    if (length(extend) == 1) {

+        extend = rep(extend, 2)

+    }

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

     sp2 <- c(sp, node)

@@ -241,7 +244,7 @@ get_cladelabel_position_ <- function(data, node, angle = "auto", extend = 0) {

     y <- y[!is.na(y)]

     mx <- max(sp.df$x, na.rm=TRUE)

-    d <- data.frame(x=mx, y=min(y) - extend, yend=max(y) + extend)

+    d <- data.frame(x=mx, y=min(y) - extend[2], yend=max(y) + extend[1])

     if (missing(angle))

         return(d)

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

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

 ##' @param align logical

 ##' @param barsize size of bar

-##' @param barextend extend bar vertically

+##' @param extend extend bar vertically

 ##' @param fontsize size of text

 ##' @param angle angle of text

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

@@ -22,7 +22,7 @@

 ##' @export

 ##' @author Guangchuang Yu

 geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

-                       align=TRUE, barsize=0.5, barextend=0, fontsize=3.88,

+                       align=TRUE, barsize=0.5, extend=0, fontsize=3.88,

                        angle=0, geom="text", hjust=0, fill=NA, family="sans",

                        parse=FALSE, ...) {

     mapping <- NULL

@@ -33,7 +33,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     inherit.aes <- FALSE

     layer_bar <- stat_stripBar(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset, align=align,

-                               size=barsize, barextend=barextend,

+                               size=barsize, barextend=extend,

                                mapping=mapping, data=data,

                                position=position, show.legend = show.legend,

                                inherit.aes = inherit.aes, na.rm=na.rm, ...)

@@ -45,14 +45,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

     if (geom == "text") {

         ## no fill parameter

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=barextend, angle=angle, family=family,

+                                    align=align, size=fontsize, barextend=extend, angle=angle, family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

     } else {

         layer_text <- stat_stripText(taxa1=taxa1, taxa2=taxa2, label=label, offset=offset+offset.text,

-                                    align=align, size=fontsize, barextend=barextend, angle=angle, fill=fill,family=family,

+                                    align=align, size=fontsize, barextend=extend, angle=angle, fill=fill,family=family,

                                     mapping=mapping, data=data, geom=geom, hjust=hjust,

                                     position=position, show.legend = show.legend,

                                     inherit.aes = inherit.aes, na.rm=na.rm, parse=parse, ...)

@@ -174,13 +174,16 @@ get_striplabel_position <- function(data, taxa1, taxa2, offset, align, barextend

 get_striplabel_position_ <- function(data, taxa1, taxa2, barextend=0) {

+    if (length(barextend) == 1) {

+        barextend <- rep(barextend, 2)

+    }

     node1 <- taxa2node(data, taxa1)

     node2 <- taxa2node(data, taxa2)

     xx <- with(data, c(x[node == node1], x[node == node2]))

     yy <- with(data, c(y[node == node1], y[node == node2]))

-    data.frame(x=max(xx), y=min(yy)-barextend, yend=max(yy)+barextend)

+    data.frame(x=max(xx), y=min(yy)-barextend[2], yend=max(yy)+barextend[1])

 }

 ## used in geom_strip, geom_taxalink

@@ -5,9 +5,9 @@

 \title{geom_strip}

 \usage{

 geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0,

-  align = TRUE, barsize = 0.5, barextend = 0, fontsize = 3.88,

-  angle = 0, geom = "text", hjust = 0, fill = NA, family = "sans",

-  parse = FALSE, ...)

+  align = TRUE, barsize = 0.5, extend = 0, fontsize = 3.88, angle = 0,

+  geom = "text", hjust = 0, fill = NA, family = "sans", parse = FALSE,

+  ...)

 }

 \arguments{

 \item{taxa1}{taxa1}

@@ -24,7 +24,7 @@ geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0,

 \item{barsize}{size of bar}

-\item{barextend}{extend bar vertically}

+\item{extend}{extend bar vertically}

 \item{fontsize}{size of text}