@@ -2,7 +2,7 @@ Package: ggtree

 Type: Package

 Title: an R package for visualization and annotation of phylogenetic trees with

     their covariates and other associated data

-Version: 1.13.1.9002

+Version: 1.13.2

 Authors@R: c(

 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),

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

@@ -1,5 +1,6 @@

-# ggtree 1.13.1.9002

+# ggtree 1.13.2

++ update rd of `facet_plot` by adding description and example (2018-07-19, Thu)

 + order by y in `facet_plot` (2018-07-09, Mon)

 + `extend` parameter in `geom_cladelabel` and `geom_strip` supports specifying

   extension of both sides (2018-07-06, Fri)

@@ -1,6 +1,9 @@

 ##' plot tree associated data in an additional panel

 ##'

 ##'

+##' 'facet_plot()' automatically re-arranges the input 'data' according to the tree structure,

+##' visualizes the 'data' on specific 'panel' using the 'geom' function with aesthetic 'mapping' and other parameters,

+##' and align the graph with the tree 'p' side by side.

 ##' @title facet_plot

 ##' @param p tree view

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

@@ -9,6 +12,11 @@

 ##' @param mapping aes mapping for 'geom'

 ##' @param ... additional parameters for 'geom'

 ##' @return ggplot object

+##' @examples

+##' tr <- rtree(10)

+##' dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))

+##' p <- ggtree(tr)

+##' facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))

 ##' @export

 ##' @author Guangchuang Yu

 facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {

@@ -20,7 +28,7 @@ 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)) {

+    if (is.null(df[[".panel"]])) {

         df[[".panel"]] <- factor("Tree")

     }

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

@@ -82,7 +82,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

     dd$x <- V2

     dd$width <- width

-

+    dd[[".panel"]] <- factor("Tree")

     if (is.null(color)) {

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

     } else {

@@ -101,6 +101,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=

             y <- max(p$data$y) + 1

         }

         mapping$y <- y

+        mapping[[".panel"]] <- factor("Tree")

         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)

     }

@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with

 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />

-[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.1-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) [![Awesome](https://cdn.rawgit.com/sindresorhus/awesome/d7305f38d29fed78fa85652e3a63e154dd8e8829/media/badge.svg)](https://awesome-r.com/#awesome-r-graphic-displays)

+[![releaseVersion](https://img.shields.io/badge/release%20version-1.12.4-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.13.2-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) [![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) [![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-2018--06--26-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

+[![platform](http://www.bioconductor.org/shields/availability/devel/ggtree.svg)](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [![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-2018--07--19-green.svg)](https://github.com/GuangchuangYu/ggtree/commits/master)

 The `ggtree` package extending the `ggplot2` package. It based on grammar of graphics and takes all the good parts of `ggplot2`. `ggtree` is designed for not only viewing phylogenetic tree but also displaying annotation data on the tree.

@@ -25,7 +25,7 @@ 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***. 2017, 8(1):28-36.

-[![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) [![Altmetric](https://img.shields.io/badge/Altmetric-321-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) [![Altmetric](https://img.shields.io/badge/Altmetric-320-green.svg?style=flat)](https://www.altmetric.com/details/10533079)

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

@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:

 ### Download stats

-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-30675/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1570/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree) [![total](https://img.shields.io/badge/downloads-31843/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1325/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)

 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>

@@ -25,6 +25,17 @@ ggplot object

 \description{

 plot tree associated data in an additional panel

 }

+\details{

+'facet_plot()' automatically re-arranges the input 'data' according to the tree structure,

+visualizes the 'data' on specific 'panel' using the 'geom' function with aesthetic 'mapping' and other parameters,

+and align the graph with the tree 'p' side by side.

+}

+\examples{

+tr <- rtree(10)

+dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))

+p <- ggtree(tr)

+facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))

+}

 \author{

 Guangchuang Yu

 }