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

 export(scaleClade)

 export(scale_color)

 export(scale_x_ggtree)

-export(set_tree_xlim)

 export(stat_balance)

 export(stat_hilight)

 export(subview)

@@ -127,6 +126,7 @@ export(theme_tree)

 export(theme_tree2)

 export(viewClade)

 export(write.jplace)

+export(xlim_tree)

 exportClasses(apeBootstrap)

 exportClasses(beast)

 exportClasses(codeml)

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

 CHANGES IN VERSION 1.7.1

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

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

+ 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

@@ -31,25 +31,14 @@ add_panel <- function(p, panel) {

 ##' set x axis limits for Tree panel

 ##'

 ##'

-##' @title set_tree_xlim

-##' @param tree_view tree view

+##' @title xlim_tree

 ##' @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)

-    }

+xlim_tree <- function(xlim) {

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

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

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

 }

@@ -195,8 +195,6 @@

             <li><a href="#application"> Application</a></li>

-            <li><a href="#helper-functions"> Helper functions</a></li>

-        

             <li><a href="#funny-stuff"> Funny stuff</a></li>

             <li><a href="#users-feedback"> User's feedback</a></li>

@@ -265,6 +263,7 @@

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/">ggtree - updating a tree view</a></li>

 <li><a href="https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree">an example of drawing beast tree using ggtree</a></li>

+<li><a href="https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/">xlim_tree: set x axis limits for only Tree panel</a></li>

 </ul>

 <h3 id="tree-annotation"><i class="fa fa-angle-double-right"></i> Tree annotation</h3>

 <ul>

@@ -287,10 +286,6 @@

 <li><a href="https://github.com/GuangchuangYu/plotTree-ggtree">ggtree version of plotTree.R</a></li>

 <li><a href="https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree">reproducible logo generated by ggtree</a></li>

 </ul>

-<h3 id="helper-functions"><i class="fa fa-angle-double-right"></i> Helper functions</h3>

-<ul>

-<li><a href="https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/">set_tree_xlim: set x axis limits for only Tree panel</a></li>

-</ul>

 <h3 id="funny-stuff"><i class="fa fa-angle-double-right"></i> Funny stuff</h3>

 <ul>

 <li><a href="https://guangchuangyu.github.io/2015/06/ggtree-with-funny-fonts">ggtree with funny fonts</a></li>

@@ -223,11 +223,11 @@

   }  

   </style>

-<div id = 'chart19ad646a81f1' class = 'rChart morris'></div>

+<div id = 'chart371c6b358a50' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart19ad646a81f1",

+ "element": "chart371c6b358a50",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -241,7 +241,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart19ad646a81f1",

+"id": "chart371c6b358a50",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -67,7 +67,7 @@

         }, 

         {

             "location": "/documentation/", 

-            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree.R\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Helper functions\n\n\n\n\nset_tree_xlim: set x axis limits for only Tree panel\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)", 

+            "text": "Vignettes\n\n\n\n\nggtree\n\n\nTree Data Import\n\n\nTree Visualization\n\n\nTree Annotation\n\n\nTree Manipulation\n\n\nAdvance Tree Annotation\n\n\nggtree utilities\n\n\n\n\n Blog posts\n\n\n News and updates\n\n\n\n\nviewing and annotating phylogenetic tree with ggtree\n\n\nggtree in Bioconductor 3.1\n\n\nBioC 3.1: NEWS of my BioC packages\n\n\nBioC 3.2: NEWS of my BioC packages\n\n\nNews of ggtree\n\n\nBioC 3.3: NEWS of my BioC packages\n\n\nBioC 3.4: NEWS of my BioC packages\n\n\nggtree paper published\n\n\n\n\n Data manipulation\n\n\n\n\nsubsetting data in ggtree\n\n\nggtree supports phylip tree format\n\n\n\n\n Tree visualization\n\n\n\n\nggtree - updating a tree view\n\n\nan example of drawing beast tree using ggtree\n\n\nxlim_tree: set x axis limits for only Tree panel\n\n\n\n\n Tree annotation\n\n\n\n\nlabel edge number in ggtree\n\n\nsubview\n\n\nAnnotate a phylogenetic tree with insets\n\n\nggtree annotate phylogenetic tree with local images\n\n\nembed images in ggplot2 via subview and annotate a phylogenetic tree with images using inset function\n\n\nidentify method for ggtree\n\n\nfacet_plot: a general solution to associate data with phylogenetic tree\n\n\n\n\n Tree manipulation\n\n\n\n\nflip and rotate branches in ggtree\n\n\n\n\n Application\n\n\n\n\nggtree for microbiome data\n\n\nggtree for outbreak data\n\n\nggtree version of plotTree.R\n\n\nreproducible logo generated by ggtree\n\n\n\n\n Funny stuff\n\n\n\n\nggtree with funny fonts\n\n\ncomic phylogenetic tree with ggtree and comicR\n\n\nuse emoji font in R\n\n\n\n\n User's feedback\n\n\n\n\ntweets of ggtree\n\n\nJoin the group chat on \n and \n\n\n\n\n Find out more on \nhttps://guangchuangyu.github.io/tags/ggtree/\n.\n\n\n Slides\n\n\n\n\nGenerating publication quality figures using R \n ggplot2\n\n\nggtree for visualization and annotation of phylogenetic trees\n\n\n\n\n Video\n\n\n\n\ninteractive clade highlighting\n\n\ninteractive rotating clades\n\n\ninteractive clade labeling\n\n\n\n\n Workflow\n\n\n\n\nrecreate a tree from a publication (\nBloom\n \net al\n, \nScience\n 2010)", 

             "title": "Documentation"

         }, 

         {

@@ -92,7 +92,7 @@

         }, 

         {

             "location": "/documentation/#tree-visualization", 

-            "text": "ggtree - updating a tree view  an example of drawing beast tree using ggtree", 

+            "text": "ggtree - updating a tree view  an example of drawing beast tree using ggtree  xlim_tree: set x axis limits for only Tree panel", 

             "title": " Tree visualization"

         }, 

         {

@@ -110,11 +110,6 @@

             "text": "ggtree for microbiome data  ggtree for outbreak data  ggtree version of plotTree.R  reproducible logo generated by ggtree", 

             "title": " Application"

         }, 

-        {

-            "location": "/documentation/#helper-functions", 

-            "text": "set_tree_xlim: set x axis limits for only Tree panel", 

-            "title": " Helper functions"

-        }, 

         {

             "location": "/documentation/#funny-stuff", 

             "text": "ggtree with funny fonts  comic phylogenetic tree with ggtree and comicR  use emoji font in R", 

@@ -202,7 +197,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart19ad646a81f1\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart19ad646a81f1\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 

+            "text": "Let us know\n if you have published using \nggtree\n and your publication will be featured here.\n\n\n\n\n\n\n\n\n\n\n\n\n\n  .rChart {\n    display: block;\n    margin-left: auto; \n    margin-right: auto;\n    width: 800px;\n    height: 300px;\n  }  \n  \n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart371c6b358a50\",\n\"width\":            800,\n\"height\":            400,\n\"xkey\": \"year\",\n\"ykeys\": [\n \"cites\" \n],\n\"data\": [\n {\n \"year\": 2016,\n\"cites\":              1,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart371c6b358a50\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n 2016\n\n\nLack of GLYCOLATE OXIDASE 1, but not GLYCOLATE OXIDASE 2, attenuates the photorespiratory phenotype of CATALASE2-deficient \nArabidopsis\n\n\nPlant Physiology\n May. 2016 \n\n\n\n\nRange overlap drives chromosome inversion fixation in passerine birds\n\n\nbioRxiv\n May. 2016 \nhttp://dx.doi.org/10.1101/053371\n\n\n\n\nPhenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape\n\n\nFront. Cell. Infect. Microbiol.\n Apr. 2016 \nhttp://dx.doi.org/10.3389%2Ffcimb.2016.00036\n\n\n\n\nWs-2\n Introgression in a Proportion of \nArabidopsis thaliana Col-0\n Stock Seed Produces Specific Phenotypes and Highlights the Importance of Routine Genetic Verification\n\n\nPlant Cell\n Mar. 2016 \nhttp://dx.doi.org/10.1105/tpc.16.00053\n\n\n\n\n 2015\n\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens\n\n\nMolecuar Ecology\n Dec. 2015 \nhttp://dx.doi.org/10.1111/mec.13474\n\n\n\n\nGenetic characterization of highly pathogenic H5 influenza viruses from poultry in Taiwan, 2015\n\n\nInfection, Genetics and Evolution\n Dec. 2015 \nhttp://dx.doi.org/10.1016/j.meegid.2015.12.006\n\n\n\n\nTrans-species polymorphism at antimicrobial innate immunity cathelicidin genes of Atlantic cod and related species\n\n\nPeerJ\n May 2015 \nhttps://doi.org/10.7717/peerj.976", 

             "title": "Featured Articles"

         }, 

         {

similarity index 67%

rename from man/set_tree_xlim.Rd

rename to man/xlim_tree.Rd

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

 % 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}

+\name{xlim_tree}

+\alias{xlim_tree}

+\title{xlim_tree}

 \usage{

-set_tree_xlim(tree_view, xlim)

+xlim_tree(xlim)

 }

 \arguments{

-\item{tree_view}{tree view}

-

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

 }

 \value{

@@ -48,6 +48,8 @@

 + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)

 + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)

++ [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)

+

 ### <i class="fa fa-angle-double-right"></i> Tree annotation

@@ -70,9 +72,6 @@

 + [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)

 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)

-### <i class="fa fa-angle-double-right"></i> Helper functions

-

-+ [set_tree_xlim: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/)

 ### <i class="fa fa-angle-double-right"></i> Funny stuff

@@ -36,10 +36,10 @@

   }  

   </style>

-<div id = 'chart19ad646a81f1' class = 'rChart morris'></div>

+<div id = 'chart371c6b358a50' class = 'rChart morris'></div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart19ad646a81f1",

+ "element": "chart371c6b358a50",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -53,7 +53,7 @@

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart19ad646a81f1",

+"id": "chart371c6b358a50",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -35,6 +35,8 @@

 + [ggtree - updating a tree view](https://guangchuangyu.github.io/2015/02/ggtree---updating-a-tree-view/)

 + [an example of drawing beast tree using ggtree](https://guangchuangyu.github.io/2015/04/an-example-of-drawing-beast-tree-using-ggtree)

++ [xlim_tree: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/xlim_tree-set-x-axis-limits-for-only-tree-panel/)

+

 ### <i class="fa fa-angle-double-right"></i> Tree annotation

@@ -57,9 +59,6 @@

 + [ggtree version of plotTree.R](https://github.com/GuangchuangYu/plotTree-ggtree)

 + [reproducible logo generated by ggtree](https://guangchuangyu.github.io/2016/10/reproducible-logo-generated-by-ggtree)

-### <i class="fa fa-angle-double-right"></i> Helper functions

-

-+ [set_tree_xlim: set x axis limits for only Tree panel](https://guangchuangyu.github.io/2016/10/set_tree_xlim-set-x-axis-limits-for-only-tree-panel/)

 ### <i class="fa fa-angle-double-right"></i> Funny stuff

similarity index 63%

rename from tests/testthat/test-set_tree_xlim.R

rename to tests/testthat/test-xlim_tree.R

@@ -1,4 +1,4 @@

-context("set_tree_xlim")

+context("xlim_tree")

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

     set.seed(2016-10-31)

@@ -8,7 +8,7 @@ test_that("dummy layer to set x axis limits of Tree panel", {

     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')

+    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

 })