@@ -117,6 +117,7 @@ export(rtree)

 export(scaleClade)

 export(scale_color)

 export(scale_x_ggtree)

+export(set_tree_xlim)

 export(stat_balance)

 export(stat_hilight)

 export(subview)

@@ -189,6 +190,7 @@ importFrom(ggplot2,element_rect)

 importFrom(ggplot2,facet_grid)

 importFrom(ggplot2,fortify)

 importFrom(ggplot2,geom_bar)

+importFrom(ggplot2,geom_blank)

 importFrom(ggplot2,geom_rect)

 importFrom(ggplot2,geom_segment)

 importFrom(ggplot2,geom_text)

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

 CHANGES IN VERSION 1.7.1

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

+ o set_tree_xlim function and test <2016-10-31, Mon>

+   + set x axis limit 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

+   + store nhx_tags$node as numeric values <2016-10-31, Mon>

  o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>

    + https://github.com/tengfei/ggbio/issues/83

  o make tree stats available in facet_plot <2016-10-24, Mon>

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

 ##' @param file nhx file

 ##' @return nhx object

 ##' @export

-##' @author Guangchuang Yu \url{http://ygc.name}

+##' @author Guangchuang Yu \url{https://guangchuangyu.github.io}

 read.nhx <- function(file) {

     treetext <- suppressWarnings(readLines(file))

     treetext <- treetext[treetext != ""]

@@ -27,7 +27,7 @@ read.nhx <- function(file) {

     phylo2 <- read.tree(text = tree2)

     treeinfo <- fortify(phylo2)

-    node <- as.character(treeinfo$node[match(nlab, sub(".+(X\\d+)$","\\1",treeinfo$label))])

+    node <- treeinfo$node[match(nlab, sub(".+(X\\d+)$","\\1",treeinfo$label))] # as.character

     nhx.matches <- gregexpr("(\\w+)?(:?\\d*\\.?\\d*[Ee]?[\\+\\-]?\\d*)?\\[&&NHX.*?\\]", treetext)

     matches <- nhx.matches[[1]]

@@ -1,6 +1,6 @@

 ##' plot tree associated data in an additional panel

 ##'

-##' 

+##'

 ##' @title facet_plot

 ##' @param p tree view

 ##' @param panel panel name for plot of input data

@@ -27,3 +27,29 @@ add_panel <- function(p, panel) {

     p$data <- df

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

 }

+

+##' set x axis limits for Tree panel

+##'

+##'

+##' @title set_tree_xlim

+##' @param tree_view tree view

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

+##' @return updated tree view

+##' @export

+##' @importFrom ggplot2 geom_blank

+##' @author guangchuang yu

+set_tree_xlim <- function(tree_view, xlim) {

+    if (length(xlim) != 2) {

+        stop('-> xlim should be of length 2...')

+    }

+    x <- tree_view$data$x

+    if (is.na(xlim[1])) {

+        xlim[1] <- min(x)

+    }

+    if (is.na(xlim[2])) {

+        xlim[2] <- max(x)

+    }

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

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

+}

+

@@ -3,7 +3,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 [![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)

-[![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--30-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--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)

 [![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)

@@ -16,6 +16,6 @@ nhx object

 read nhx tree file

 }

 \author{

-Guangchuang Yu \url{http://ygc.name}

+Guangchuang Yu \url{https://guangchuangyu.github.io}

 }

new file mode 100644

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

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/facet_plot.R

+\name{set_tree_xlim}

+\alias{set_tree_xlim}

+\title{set_tree_xlim}

+\usage{

+set_tree_xlim(tree_view, xlim)

+}

+\arguments{

+\item{tree_view}{tree view}

+

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

+}

+\value{

+updated tree view

+}

+\description{

+set x axis limits for Tree panel

+}

+\author{

+guangchuang yu

+}

+

new file mode 100644

@@ -0,0 +1,14 @@

+context("set_tree_xlim")

+

+test_that("dummy layer to set x axis limits of Tree panel", {

+    set.seed(2016-10-31)

+    tr <- rtree(50)

+    tr$tip.label <- paste(tr$tip.label, tr$tip.label, sep="_")

+    p <- ggtree(tr) + geom_tiplab(align=TRUE) + theme_tree2()

+

+    d <- data.frame(id = tr$tip.label, v= rnorm(50))

+

+    p2 <- facet_plot(set_tree_xlim(p, c(NA, 6)), geom=geom_point, data=d, mapping=aes(x=v), panel='dot') + ggtitle('*set_tree_xlim* only change x axis limits of *Tree* panel')

+

+    expect_true(is.ggplot(p2)) # should plot appropriately

+})