@@ -3,7 +3,7 @@ Type: Package

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

 Version: 1.7.2

 Authors@R: c(

-	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),

+	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")),

 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")),

 	   person("Justin", "Silverman", email = "jsilve24@gmail.com", rol = "ctb", comment = "geom_balance"),

 	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb",

@@ -40,6 +40,7 @@ export(collapse)

 export(decimal2Date)

 export(download.phylopic)

 export(expand)

+export(expand_xlim)

 export(facet_plot)

 export(flip)

 export(geom_aline)

@@ -1,12 +1,14 @@

 CHANGES IN VERSION 1.7.2

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

+ o expand_xlim for setting x axis limits of specific panel <2016-11-01, Tue>

+   + xlim_tree is now a specific case of expand_xlim(xlim, panel='Tree')

  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>

    + https://github.com/GuangchuangYu/ggtree/issues/84

 CHANGES IN VERSION 1.7.1

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

  o xlim_tree layer and test <2016-10-31, Mon>

-   + set x axis limit for Tree panel for facet_plot

+   + set x axis limits for Tree panel for facet_plot

  o update read.nhx <2016-10-30, Sun>

    + add tip numbers to @nhx_tags and add tests

    + https://github.com/GuangchuangYu/ggtree/pull/83

@@ -20,25 +20,11 @@ facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {

 ##' @importFrom ggplot2 facet_grid

 add_panel <- function(p, panel) {

     df <- p$data

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

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

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

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

     }

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

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

     p$data <- df

-    p + facet_grid(.~panel, scales="free_x")

-}

-

-##' set x axis limits for Tree panel

-##'

-##'

-##' @title xlim_tree

-##' @param xlim xlim, should be of length 2

-##' @return updated tree view

-##' @export

-##' @importFrom ggplot2 geom_blank

-##' @author guangchuang yu

-xlim_tree <- function(xlim) {

-    dummy <- data.frame(x=xlim, panel='Tree')

-    geom_blank(aes_(x=~x), dummy, inherit.aes = FALSE)

+    p + facet_grid(.~.panel, scales="free_x")

 }

@@ -100,19 +100,19 @@

 ##' @author Guangchuang Yu

 `%+>%` <- function(p, data) {

     df <- p$data

-    lv <- levels(df$panel)

+    lv <- levels(df$.panel)

     if (is(data, "GRanges") || is(data, "GRangesList")) {

         names(data) <- df$y[match(names(data), df$label)]

         res <- data[order(as.numeric(names(data)))]

         mcols <- get_fun_from_pkg("GenomicRanges", "mcols")

         `mcols<-` <- get_fun_from_pkg("GenomicRanges", "`mcols<-`")

-        mcols(res)$panel <- factor(lv[length(lv)], levels=lv)

+        mcols(res)$.panel <- factor(lv[length(lv)], levels=lv)

     } else if (is(data, "data.frame") || is(data, "tbl_df")) {

         data <- as.data.frame(data)

         ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)

         res <- merge(df[, !names(df) %in% c('node', 'parent', 'x', 'branch', 'angle')], data, by.x='label', by.y=1)

-        res$panel <- factor(lv[length(lv)], levels=lv)

+        res$.panel <- factor(lv[length(lv)], levels=lv)

     } else {

         stop("input 'data' is not supported...")

     }

new file mode 100644

@@ -0,0 +1,28 @@

+##' set x axis limits for Tree panel

+##'

+##'

+##' @title xlim_tree

+##' @param xlim xlim

+##' @return updated tree view

+##' @export

+##' @author guangchuang yu

+xlim_tree <- function(xlim) {

+    expand_xlim(xlim, panel='Tree')

+}

+

+

+##' expand x axis limits for specific panel

+##'

+##'

+##' @title expand_xlim

+##' @param xlim xlim

+##' @param panel panel

+##' @return updated tree view

+##' @importFrom ggplot2 geom_blank

+##' @export

+##' @author guangchuang yu

+expand_xlim <- function(xlim, panel) {

+    dummy <- data.frame(x=xlim, .panel=panel)

+    geom_blank(aes_(x=~x), dummy, inherit.aes = FALSE)

+}

+

@@ -1,9 +1,9 @@

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

 ===========================================================================================================================

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.1-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-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.2-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-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/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-2016--10--31-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-2016--11--01-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) [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-green.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html)

new file mode 100644

@@ -0,0 +1,23 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/xlim.R

+\name{expand_xlim}

+\alias{expand_xlim}

+\title{expand_xlim}

+\usage{

+expand_xlim(xlim, panel)

+}

+\arguments{

+\item{xlim}{xlim}

+

+\item{panel}{panel}

+}

+\value{

+updated tree view

+}

+\description{

+expand x axis limits for specific panel

+}

+\author{

+guangchuang yu

+}

+

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

 % Generated by roxygen2: do not edit by hand

-% Please edit documentation in R/facet_plot.R

+% Please edit documentation in R/xlim.R

 \name{xlim_tree}

 \alias{xlim_tree}

 \title{xlim_tree}

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

 xlim_tree(xlim)

 }

 \arguments{

-\item{xlim}{xlim, should be of length 2}

+\item{xlim}{xlim}

 }

 \value{

 updated tree view