@@ -7,3 +7,5 @@ TODO.md

 appveyor.yml

 Makefile

 README.Rmd

+mkdocs

+docs

@@ -4,3 +4,5 @@ vignettes/.DS_Store

 *~

 *.Rhistory

 .svn

+__init__.py

+__pycache__

@@ -6,3 +6,5 @@ TODO.md

 appveyor.yml

 .travis.yml

 README.Rmd

+docs

+mkdocs

@@ -1,5 +1,8 @@

 CHANGES IN VERSION 1.5.11

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

+ o gheatmap works with matrix <2016-08-28, Sun>

+   + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/2YLvXHMJJ6U/c4zS7yfGCAAJ

+ o support parsing expression in geom_strip <2016-08-18, Thu>

  o bug fixed in geom_tiplab <2016-08-17, Wed>

    + https://groups.google.com/forum/?utm_medium=email&utm_source=footer#!msg/bioc-ggtree/Tm9ULK7hd9E/HviXEh3CBwAJ

  o update citation info, add doi. <2016-08-16, Tue>

@@ -16,13 +16,15 @@

 ##' @param hjust hjust

 ##' @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

 ##' @return ggplot layers

 ##' @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,

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

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

+                       parse=FALSE, ...) {

     mapping <- NULL

     data <- NULL

     position <- "identity"

@@ -46,14 +48,14 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

                                     align=align, size=fontsize, barextend=barextend, 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, ...)

+                                    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,

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

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

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

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

     }

     list(

@@ -66,7 +68,7 @@ geom_strip <- function(taxa1, taxa2, label=NA, offset=0, offset.text=0,

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

                            geom="text", position="identity",

                            taxa1, taxa2, label, offset, align, barextend, ...,

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

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

     if (is.null(label) || is.na(label)) {

         default_aes <- aes_(x=~x, y=~y, node=~node, label=~label)

@@ -94,6 +96,7 @@ stat_stripText <- function(mapping=NULL, data=NULL,

                       align=align,

                       barextend=barextend,

                       na.rm=na.rm,

+                      parse=parse,

                       ...)

           )

@@ -43,7 +43,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     df <- df[df$isTip,]

     start <- max(df$x) + offset

-    dd <- data

+    dd <- as.data.frame(data)

     ## dd$lab <- rownames(dd)

     lab <- df$label[order(df$y)]

     dd <- dd[lab, , drop=FALSE]

@@ -3,9 +3,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 [![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)

-[![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-2016--08--17-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)

+[![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-2016--08--18-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master) [![commit](http://www.bioconductor.org/shields/commits/bioc/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#svn_source) [![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)

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.16-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.11-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.4.17-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.5.11-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) [![post](http://www.bioconductor.org/shields/posts/ggtree.svg)](https://support.bioconductor.org/t/ggtree/) [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/)

 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

@@ -32,12 +32,6 @@ For details, please visit our project website, <https://guangchuangyu.github.io/

 [![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-12113/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![month](https://img.shields.io/badge/downloads-1091/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree/)

-    If you use ggtree in published research, please cite:

-

-    Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam.

-    ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data.

-    Methods in Ecology and Evolution 2016, doi:10.1111/2041-210X.12628

-

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

          |                                                                                    *        |

     1200 +                                                                                             +

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

 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, ...)

 }

 \arguments{

 \item{taxa1}{taxa1}

@@ -38,6 +38,8 @@ geom_strip(taxa1, taxa2, label = NA, offset = 0, offset.text = 0,

 \item{family}{sans by default, can be any supported font}

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

+

 \item{...}{additional parameter}

 }

 \value{