@@ -4,10 +4,11 @@ Title: an R package for visualization and annotation of phylogenetic trees with

 Version: 1.7.1

 Authors@R: c(

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

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

+	   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",

-	          comment = "propose using txtConnection so that parser functions can use tree strings as input")

+	          comment = c("propose using txtConnection so that parser functions can use tree strings as input",

+		  "modified nhx parsing to retain tip node numbers"))

 	   )

 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>

 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.

@@ -126,6 +126,7 @@ export(theme_tree)

 export(theme_tree2)

 export(viewClade)

 export(write.jplace)

+export(xlim_tree)

 exportClasses(apeBootstrap)

 exportClasses(beast)

 exportClasses(codeml)

@@ -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 xlim_tree layer 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$node[match(nlab, treeinfo$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 +27,18 @@ add_panel <- function(p, 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)

+}

+

@@ -111,7 +111,7 @@

     } 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, 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)

     } else {

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

@@ -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--26-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)

@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`:

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. ***Methods in Ecology and Evolution***. *accepted*

-[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-250-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![doi](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-green.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628) [![citation](https://img.shields.io/badge/cited%20by-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-275-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -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 +1,21 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/facet_plot.R

+\name{xlim_tree}

+\alias{xlim_tree}

+\title{xlim_tree}

+\usage{

+xlim_tree(xlim)

+}

+\arguments{

+\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 +1,77 @@

+context('nhx')

+

+# Some sample NHX tree strings

+test_nhx_text = "(((ADH2:0.1[&&NHX:S=human], ADH1:0.11[&&NHX:S=human]):0.05[&&NHX:S=primates:D=Y:B=100], ADHY:0.1[&&NHX:S=nematode],ADHX:0.12[&&NHX:S=insect]):0.1[&&NHX:S=metazoa:D=N], (ADH4:0.09[&&NHX:S=yeast],ADH3:0.13[&&NHX:S=yeast], ADH2:0.12[&&NHX:S=yeast],ADH1:0.11[&&NHX:S=yeast]):0.1 [&&NHX:S=Fungi])[&&NHX:D=N];"

+

+test_phyldog_nhx_text = "(((Prayidae_D27SS7@2825365:0.0682841[&&NHX:Ev=S:S=58:ND=0],(Kephyes_ovata@2606431:0.0193941[&&NHX:Ev=S:S=69:ND=1],Chuniphyes_multidentata@1277217:0.0121378[&&NHX:Ev=S:S=70:ND=2]):0.0217782[&&NHX:Ev=S:S=60:ND=3]):0.0607598[&&NHX:Ev=S:S=36:ND=4],((Apolemia_sp_@1353964:0.11832[&&NHX:Ev=S:S=31:ND=9],(((Bargmannia_amoena@263997:0.0144549[&&NHX:Ev=S:S=37:ND=10],Bargmannia_elongata@946788:0.0149723[&&NHX:Ev=S:S=38:ND=11]):0.0925388[&&NHX:Ev=S:S=33:ND=12],Physonect_sp_@2066767:0.077429[&&NHX:Ev=S:S=61:ND=13]):0.0274637[&&NHX:Ev=S:S=24:ND=14],(Stephalia_dilata@2960089:0.0761163[&&NHX:Ev=S:S=52:ND=15],((Frillagalma_vityazi@1155031:0.0906068[&&NHX:Ev=S:S=53:ND=16],Resomia_ornicephala@3111757:1e-06[&&NHX:Ev=S:S=54:ND=17]):1e-06[&&NHX:Ev=S:S=45:ND=18],((Lychnagalma_utricularia@2253871:0.120851[&&NHX:Ev=S:S=65:ND=19],Nanomia_bijuga@717864:0.133939[&&NHX:Ev=S:S=71:ND=20]):1e-06[&&NHX:Ev=S:S=56:ND=21],Cordagalma_sp_@1525873:0.0693814[&&NHX:Ev=S:S=64:ND=22]):1e-06[&&NHX:Ev=S:S=46:ND=23]):0.0333823[&&NHX:Ev=S:S=40:ND=24]):1e-06[&&NHX:Ev=S:S=35:ND=25]):0.0431861[&&NHX:Ev=D:S=24:ND=26]):1e-06[&&NHX:Ev=S:S=19:ND=27],Rhizophysa_filiformis@3073669:0.22283[&&NHX:Ev=S:S=26:ND=28]):0.0292362[&&NHX:Ev=S:S=17:ND=29]):0.185603[&&NHX:Ev=D:S=17:ND=8],(Hydra_magnipapillata@52244:0.0621782[&&NHX:Ev=S:S=16:ND=5],Ectopleura_larynx@3556167:0.332505[&&NHX:Ev=S:S=15:ND=6]):0.185603[&&NHX:Ev=S:S=12:ND=7])[&&NHX:Ev=S:S=9:ND=30];"

+

+test_notung_nhx_text = "((((Rhizophysa_filiformis@2564549:0.09666991738603078[&&NHX:S=Rhizophysa_filiformis],((Marrus_claudanielis@2027078:0.03368582974818837[&&NHX:S=Marrus_claudanielis],((Erenna_richardi@1434201:0.014306889954561298[&&NHX:S=Erenna_richardi],Marrus_claudanielis@2027079:0.010842363778569869[&&NHX:S=Marrus_claudanielis])n5940011:0.01779384958849464[&&NHX:S=n57:D=N],(((Agalma_elegans@88626:0.05872379503260147[&&NHX:S=Agalma_elegans],Lychnagalma_utricularia@1828459:0.04211137470826968[&&NHX:S=Lychnagalma_utricularia])n5940018:0.02375590664436535[&&NHX:S=n47:D=N],(((Bargmannia_amoena@3459111:0.19058396964770352[&&NHX:S=Bargmannia_amoena],Bargmannia_elongata@469437:1.00000050002909E-6[&&NHX:S=Bargmannia_elongata])n5939974:0.11560220708003867[&&NHX:S=n22:D=N],Cordagalma_sp_@1115328:0.04829417133033771[&&NHX:S=Cordagalma_sp_])n5939976:0.011316847557531757[&&NHX:S=n62:D=N],Forskalia_asymmetrica@1220430:0.01667566952752948[&&NHX:S=Forskalia_asymmetrica])n5939978:0.0063213422810751655[&&NHX:S=n62:D=Y])n5940014:0.017792661031819083[&&NHX:S=n62:D=Y],(Resomia_ornicephala@2657185:0.004262563771468986[&&NHX:S=Resomia_ornicephala],Frillagalma_vityazi@663744:0.028441637105547157[&&NHX:S=Frillagalma_vityazi])n5939981:0.006136291467151878[&&NHX:S=n51:D=N])n5940013:0.013546839136761205[&&NHX:S=n62:D=Y])n5940012:0.011839606018978143[&&NHX:S=n62:D=Y])n5940008:0.013840645450221475[&&NHX:S=n62:D=Y],(((Chelophyes_appendiculata@1615707:0.007647023552225329[&&NHX:S=Chelophyes_appendiculata],Clytia_hemisphaerica@756642:0.643907456299178[&&NHX:S=Clytia_hemisphaerica])n5939984:0.08603691877960613[&&NHX:S=n67:D=N],(Chuniphyes_multidentata@930929:0.01248550133310033[&&NHX:S=Chuniphyes_multidentata],Kephyes_ovata@1966030:0.014671165587181996[&&NHX:S=Kephyes_ovata])n5939987:0.013285803501636162[&&NHX:S=n27:D=N])n5939988:0.008000411801689693[&&NHX:S=n67:D=Y],(((Hippopodius_hippopus@1084434:0.0505718831943577[&&NHX:S=Hippopodius_hippopus],Prayidae_D27D2@2878798:0.00905875758406546[&&NHX:S=Prayidae_D27D2])n5939991:0.021772123626769023[&&NHX:S=n38:D=N],Prayidae_D27SS7@2181711:0.029009000260863272[&&NHX:S=Prayidae_D27SS7])n5939993:1.00000050002909E-6[&&NHX:S=n38:D=Y],Prayidae_D27D2@2878801:1.00000050002909E-6[&&NHX:S=Prayidae_D27D2])n5939995:0.00916688375355408[&&NHX:S=n38:D=Y])n5939996:0.05191099091093772[&&NHX:S=n67:D=Y])n5940006:0.03953811931719265[&&NHX:S=n67:D=Y])n5940005:0.10134081070615458[&&NHX:S=n67:D=Y],(Podocoryna_carnea@3033951:0.11270255504816476[&&NHX:S=Podocoryna_carnea],Hydractinia_symbiolongicarpus@1679508:0.030168043235021993[&&NHX:S=Hydractinia_symbiolongicarpus])n5939999:0.17223048099362362[&&NHX:S=n11:D=N])n5940003:0.16233679521228994[&&NHX:S=n67:D=Y],Hydra_magnipapillata@801936:0.585696573276294[&&NHX:S=Hydra_magnipapillata])n5940002:0.4403044529817829[&&NHX:S=n68:D=N],Aegina_citrea@825314:0.4403044529817829[&&NHX:S=Aegina_citrea])n5942419[&&NHX:S=n70:D=N];"

+

+# A function to simplify NHX text so that it can be parsed by 

+# ape::read.tree(). Discards much useful information. Intent is to 

+# be able to compare node annotations that have been independently

+# parsed with different methods. 

+simplify_nhx_string <- function( text ){

+	# Remove branch lengths so NHX tags are adjacent to nodes

+	# Accommodate lengths in scientific notation, eg 1e-6

+	text = gsub( "\\:[\\d\\.]+e[\\d\\-]+","", text, perl=TRUE )

+	text = gsub( "\\:[\\d\\.]+","", text, perl=TRUE )

+	

+	# Remove NHX tags at tips

+	text = gsub( "([^\\)])\\[.+?\\]","\\1", text, perl=TRUE )

+

+	# Remove brackets

+	text = gsub( "\\[&&NHX:","", text, perl=TRUE )

+	text = gsub( "\\]","", text, perl=TRUE )

+

+	# Replace NHX tag formatting characters that aren't allowed

+	text = gsub( ":","_", text, perl=TRUE )

+	text = gsub( "=","-", text, perl=TRUE )

+	

+	return(text)

+}

+

+

+test_that("can parse example ggtree nhx tree string", {

+	nhx <- read.nhx( textConnection(test_nhx_text) )

+	ntips = length(nhx@phylo$tip.label)

+

+	# Correct number of tips

+	expect_equal( ntips , 8 )

+

+	# All node numbers, including tips, are parsed

+	expect_true( all(!is.na(nhx@nhx_tags$node)) )

+})

+

+test_that("can parse phyldog nhx tree string", {

+	nhx <- read.nhx( textConnection(test_phyldog_nhx_text) )

+	ntips = length(nhx@phylo$tip.label)

+

+	# Correct number of tips

+	expect_equal( ntips , 16 )

+

+	# All node numbers, including tips, are parsed

+	expect_true( all(!is.na(nhx@nhx_tags$node)) )

+

+	# Verify that the S field of internal nodes was correctly parsed

+	# Assumes that node identity order is the same between phy and nhx@phylo

+	tags = nhx@nhx_tags

+	tags$node = as.numeric(tags$node)

+	tags = tags[order(tags$node),]

+	internal_tags = tags[ tags$node > length(nhx@phylo$tip.label), ] # Consider internal nodes only

+

+

+	phy = read.tree(text=simplify_nhx_string(test_phyldog_nhx_text))

+	phy_S=unlist(lapply(strsplit(phy$node.label, "_"), function(x) x[[2]])) # Get the S field

+	phy_S=unlist(lapply(strsplit(phy_S, "-"), function(x) x[[2]])) # Get the value

+	phy_S=as.numeric(phy_S)

+	expect_equal( phy_S, as.numeric(internal_tags$S) )

+

+	# Verify that S fild of tips was correctly parsed

+	# by comparison against expected values

+	tip_tags = tags[1:length(nhx@phylo$tip.label),]

+	tip.labels = c("Prayidae_D27SS7@2825365", "Kephyes_ovata@2606431", "Chuniphyes_multidentata@1277217", "Apolemia_sp_@1353964", "Bargmannia_amoena@263997", "Bargmannia_elongata@946788", "Physonect_sp_@2066767", "Stephalia_dilata@2960089", "Frillagalma_vityazi@1155031", "Resomia_ornicephala@3111757", "Lychnagalma_utricularia@2253871", "Nanomia_bijuga@717864", "Cordagalma_sp_@1525873", "Rhizophysa_filiformis@3073669", "Hydra_magnipapillata@52244", "Ectopleura_larynx@3556167")

+	S.tip.values = c(58, 69, 70, 31, 37, 38, 61, 52, 53, 54, 65, 71, 64, 26, 16, 15)

+	expect_equal( S.tip.values[match(nhx@phylo$tip.label, tip.labels)], as.numeric(tip_tags$S))

+

+})

\ No newline at end of file

new file mode 100644

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

+context("xlim_tree")

+

+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(p + xlim_tree(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

+})