@@ -1,3 +1,4 @@

+

 Justin Silverman

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

 + `geom_balance`

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

 ##' append a heatmap of a matrix to right side of phylogenetic tree

 ##'

-##' 

+##'

 ##' @title gheatmap

 ##' @param p tree view

 ##' @param data matrix or data.frame

@@ -31,23 +31,23 @@

 gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color="white",

                      colnames=TRUE, colnames_position="bottom", colnames_angle=0, colnames_level=NULL,

                      colnames_offset_x = 0, colnames_offset_y = 0, font.size=4, hjust=0.5) {

-    

+

     colnames_position %<>% match.arg(c("bottom", "top"))

     variable <- value <- lab <- y <- NULL

-    

+

     ## if (is.null(width)) {

     ##     width <- (p$data$x %>% range %>% diff)/30

     ## }

-    

+

     ## convert width to width of each cell

     width <- width * (p$data$x %>% range %>% diff) / ncol(data)

-    

+

     isTip <- x <- y <- variable <- value <- from <- to <- NULL

-    

+

     df <- p$data

     df <- df[df$isTip,]

     start <- max(df$x) + offset

-    

+

     dd <- as.data.frame(data)

     ## dd$lab <- rownames(dd)

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

@@ -69,10 +69,10 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     V2 <- start + as.numeric(dd$variable) * width

     mapping <- data.frame(from=dd$variable, to=V2)

     mapping <- unique(mapping)

-    

+

     dd$x <- V2

     dd$width <- width

-    

+

     if (is.null(color)) {

         p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)

     } else {

@@ -83,7 +83,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     } else {

         p2 <- p2 + scale_fill_discrete(na.value=NA) #"white")

     }

-    

+

     if (colnames) {

         if (colnames_position == "bottom") {

             y <- 0

@@ -94,10 +94,10 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

         p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), size=font.size, inherit.aes = FALSE,

                              angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)

     }

-    

+

     p2 <- p2 + theme(legend.position="right", legend.title=element_blank())

     ## p2 <- p2 + guides(fill = guide_legend(override.aes = list(colour = NULL)))

-    

+

     attr(p2, "mapping") <- mapping

     return(p2)

 }

@@ -234,12 +234,12 @@ published using <code>ggtree</code> and your publication will be featured here.<

     height: 300px;

   }<br />

   </style>

-<div id="chart5f2d37e8c08a" class="rChart morris"></p>

+<div id="chart11855a166b40" class="rChart morris"></p>

 </div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart5f2d37e8c08a",

+ "element": "chart11855a166b40",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -258,7 +258,7 @@ published using <code>ggtree</code> and your publication will be featured here.<

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart5f2d37e8c08a",

+"id": "chart11855a166b40",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -234,7 +234,7 @@

 <link rel="stylesheet" href="https://guangchuangyu.github.io/css/academicons.min.css"></p>

 <p><a href="https://bioconductor.org/packages/ggtree"><img alt="" src="https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat" /></a>

 <a href="https://github.com/guangchuangyu/ggtree"><img alt="" src="https://img.shields.io/badge/devel%20version-1.9.1-blue.svg?style=flat" /></a>

-<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-16372/total-blue.svg?style=flat" /></a>

+<a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-16674/total-blue.svg?style=flat" /></a>

 <a href="https://bioconductor.org/packages/stats/bioc/ggtree"><img alt="" src="https://img.shields.io/badge/download-1117/month-blue.svg?style=flat" /></a></p>

 <p>The <code>ggtree</code> package extending the <em>ggplot2</em> package. It based on

 grammar of graphics and takes all the good parts of <em>ggplot2</em>. <em>ggtree</em>

@@ -256,7 +256,7 @@ University of Hong Kong.</p>

 <h2 id="citation"><i class="fa fa-book"></i> Citation</h2>

 <p>Please cite the following article when using <code>ggtree</code>:</p>

 <p><a href="http://dx.doi.org/10.1111/2041-210X.12628"><img alt="" src="https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat" /></a>

-<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat" /></a>

+<a href="https://www.altmetric.com/details/10533079"><img alt="" src="https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat" /></a>

 <a href="https://scholar.google.com.hk/scholar?oi=bibs&amp;hl=en&amp;cites=7268358477862164627"><img alt="citation" src="https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat" /></a></p>

 <p><strong>G Yu</strong>, DK Smith, H Zhu, Y Guan, TTY Lam<sup>*</sup>. ggtree: an R

 package for visualization and annotation of phylogenetic trees with

@@ -217,7 +217,7 @@

         }, 

         {

             "location": "/featuredArticles/", 

-            "text": "Let us know\n if you have\npublished 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  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart5f2d37e8c08a\",\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 \"year\": 2017,\n\"cites\":             21,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart5f2d37e8c08a\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.", 

+            "text": "Let us know\n if you have\npublished 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  }<br />\n  \n\n\n\n\n\n\n\n\n    var chartParams = {\n \"element\": \"chart11855a166b40\",\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 \"year\": 2017,\n\"cites\":             21,\n\"pubid\": \"HtEfBTGE9r8C\" \n} \n],\n\"id\": \"chart11855a166b40\",\n\"labels\": \"cites\" \n},\n      chartType = \"Bar\"\n    new Morris[chartType](chartParams)\n\n\n\n\n\n\n\n\n\n\n 2017\n\n\nPhylogenetic analysis of the human antibody repertoire reveals\nquantitative signatures of immune senescence and\naging\n. \nPNAS\n, 2017\n\n\nHorses in Denmark Are a Reservoir of Diverse Clones of\nMethicillin-Resistant and -Susceptible Staphylococcus\naureus\n.\n\nFrontiers in Microbiology\n, 2017, 8:543\n\n\nGut metagenomes of type 2 diabetic patients have characteristic\nsingle-nucleotide polymorphism distribution in \nBacteroides\ncoprocola\n.\n\nMicrobiome\n, 2017, 5:15\n\n\n 2016\n\n\nFunction and Phylogeny of Bacterial Butyryl Coenzyme A:Acetate\nTransferases and Their Diversity in the Proximal Colon of\nSwine\n. \nApplied and\nEnvironmental Microbiology\n. 2016, 82(22):6788-6798.", 

             "title": "Featured Articles"

         }, 

         {

@@ -4,7 +4,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -12,7 +12,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/documentation/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -20,7 +20,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/faq/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -28,7 +28,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/featuredArticles/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -36,7 +36,7 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/gallery/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -45,55 +45,55 @@

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ChIPseeker/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/clusterProfiler/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/DOSE/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/emojifont/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ggtree/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/GOSemSim/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/meshes/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/ReactomePA/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

     <url>

      <loc>https://guangchuangyu.github.io/ggtree/treeio/</loc>

-     <lastmod>2017-06-19</lastmod>

+     <lastmod>2017-06-28</lastmod>

      <changefreq>daily</changefreq>

     </url>

@@ -39,13 +39,13 @@ published using `ggtree` and your publication will be featured here.

     height: 300px;

   }  

   </style>

-<div id="chart5f2d37e8c08a" class="rChart morris">

+<div id="chart11855a166b40" class="rChart morris">

 </div>

 <script type='text/javascript'>

     var chartParams = {

- "element": "chart5f2d37e8c08a",

+ "element": "chart11855a166b40",

 "width":            800,

 "height":            400,

 "xkey": "year",

@@ -64,7 +64,7 @@ published using `ggtree` and your publication will be featured here.

 "pubid": "HtEfBTGE9r8C" 

 } 

 ],

-"id": "chart5f2d37e8c08a",

+"id": "chart11855a166b40",

 "labels": "cites" 

 },

       chartType = "Bar"

@@ -29,7 +29,7 @@ ggtree: visualization and annotation of phylogenetic trees

 [![](https://img.shields.io/badge/release%20version-1.8.1-blue.svg?style=flat)](https://bioconductor.org/packages/ggtree)

 [![](https://img.shields.io/badge/devel%20version-1.9.1-blue.svg?style=flat)](https://github.com/guangchuangyu/ggtree)

-[![](https://img.shields.io/badge/download-16372/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![](https://img.shields.io/badge/download-16674/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 [![](https://img.shields.io/badge/download-1117/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 The `ggtree` package extending the *ggplot2* package. It based on

@@ -60,7 +60,7 @@ University of Hong Kong.

 Please cite the following article when using `ggtree`:

 [![](https://img.shields.io/badge/doi-10.1111/2041--210X.12628-blue.svg?style=flat)](http://dx.doi.org/10.1111/2041-210X.12628)

-[![](https://img.shields.io/badge/Altmetric-346-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

+[![](https://img.shields.io/badge/Altmetric-345-blue.svg?style=flat)](https://www.altmetric.com/details/10533079)

 [![citation](https://img.shields.io/badge/cited%20by-22-blue.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627)

 **G Yu**, DK Smith, H Zhu, Y Guan, TTY Lam<sup>\*</sup>. ggtree: an R