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

 Package: ggtree

 Type: Package

 Title: a phylogenetic tree viewer for different types of tree annotations

-Version: 1.1.3

+Version: 1.1.4

 Author: Guangchuang Yu and Tommy Tsan-Yuk Lam

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: ggtree extends the ggplot2 plotting system which implemented the

@@ -14,6 +14,7 @@ export("%<%")

 export("%<+%")

 export("%>%")

 export(.)

+export(add_colorbar)

 export(aes)

 export(as.binary)

 export(collapse)

@@ -113,6 +114,8 @@ importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

 importFrom(ggplot2,geom_tile)

 importFrom(ggplot2,ggplot)

+importFrom(ggplot2,guide_legend)

+importFrom(ggplot2,guides)

 importFrom(ggplot2,labs)

 importFrom(ggplot2,scale_color_manual)

 importFrom(ggplot2,scale_fill_discrete)

@@ -1,5 +1,11 @@

+CHANGES IN VERSION 1.1.4

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

+ o add_colorbar function <2015-04-30, Thu>

+ 

 CHANGES IN VERSION 1.1.3

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

+ o add space between residue substitution (e.g. K123R / E155D) <2015-04-30, Thu>

+ o remove slash line in heatmap legend <2015-04-30, Thu>

  o update vignette to add example of merge_tree <2015-04-29, Wed>

 CHANGES IN VERSION 1.1.2

@@ -375,3 +375,38 @@ expand <- function(tree_view, node) {

     attr(tree_view, clade) <- NULL

     tree_view

 }

+

+##' add colorbar legend

+##'

+##' 

+##' @title add_colorbar

+##' @param p tree view

+##' @param color output of scale_color function

+##' @param x x position

+##' @param ymin ymin

+##' @param ymax ymax

+##' @param font.size font size 

+##' @return ggplot2 object

+##' @export

+##' @importFrom ggplot2 annotate

+##' @author Guangchuang Yu

+add_colorbar <- function(p, color, x, ymin, ymax, font.size=4) {

+    legend <- do.call("cbind", attr(color, "scale"))

+    

+    legend[,1] <- round(as.numeric(legend[,1]), 2)

+    

+    ## legend[nrow(legend),1] <- paste(">=", legend[nrow(legend),1])

+    

+    yy <- seq(ymin, ymax, length.out=nrow(legend)+1)

+

+    ymin <- yy[1:nrow(legend)]

+    ymax <- yy[2:length(yy)]

+    y <- (ymin+ymax)/2

+

+    i <- seq(1, length(y), length.out = 5) %>% round(0)

+    offset <- diff(range(p$data$x))/40

+    p + annotate("text", x=x+offset*2, y=y[i], label=legend[i,1], size=font.size) +

+        annotate("rect", xmin=x, xmax=x+offset, ymin=ymin,

+                 ymax = ymax, fill=legend[,2], color=legend[,2]) 

+    

+}

@@ -38,6 +38,8 @@ gplot <- function(p, data, low="green", high="red", widths=c(0.5, 0.5), font.siz

 ##' @importFrom ggplot2 element_text

 ##' @importFrom ggplot2 geom_tile

 ##' @importFrom ggplot2 labs

+##' @importFrom ggplot2 guides

+##' @importFrom ggplot2 guide_legend

 ##' @importFrom reshape2 melt

 gplot.heatmap <- function(p, data, low, high, font.size) {

     isTip <- x <- Var1 <- Var2 <- value <- NULL

@@ -75,6 +77,7 @@ gplot.heatmap <- function(p, data, low, high, font.size) {

     p2 <- p2 + theme(panel.margin=unit(0, "null"))

     p2 <- p2 + theme(plot.margin = unit(c(1, 1, .5, -0.5), "lines"))

     p2 <- p2 + theme(legend.position = "right")

+    p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

     ## p2 <- p2 + labs(fill="")

     return(p2)

@@ -167,7 +167,7 @@ getSubsLabel <- function(seqs, A, B, translate, removeGap) {

         return(NULL)

     }

-    res <- paste(AA[ii], ii, BB[ii], sep="", collapse="/")

+    res <- paste(AA[ii], ii, BB[ii], sep="", collapse=" / ")

     return(res)

 }

new file mode 100644

@@ -0,0 +1,31 @@

+% Generated by roxygen2 (4.1.1): do not edit by hand

+% Please edit documentation in R/ggtree.R

+\name{add_colorbar}

+\alias{add_colorbar}

+\title{add_colorbar}

+\usage{

+add_colorbar(p, color, x, ymin, ymax, font.size = 4)

+}

+\arguments{

+\item{p}{tree view}

+

+\item{color}{output of scale_color function}

+

+\item{x}{x position}

+

+\item{ymin}{ymin}

+

+\item{ymax}{ymax}

+

+\item{font.size}{font size}

+}

+\value{

+ggplot2 object

+}

+\description{

+add colorbar legend

+}

+\author{

+Guangchuang Yu

+}

+