1. ggtree
  2. Commit 6cd5161c44593c9c4c9529a90bae890070f530f2
Browse code

update rd

guangchuang yu authored on 19/07/2018 13:53:21
Showing 6 changed files
DESCRIPTION
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@@ -2,7 +2,7 @@ Package: ggtree
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 Type: Package
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 Title: an R package for visualization and annotation of phylogenetic trees with
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     their covariates and other associated data
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-Version: 1.13.1.9002
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+Version: 1.13.2
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 Authors@R: c(
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 	   person("Guangchuang", "Yu",     email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph"), comment = c(ORCID = "0000-0002-6485-8781")),
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 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com",   role = c("aut", "ths")),
NEWS.md
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@@ -1,5 +1,6 @@
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-# ggtree 1.13.1.9002
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+# ggtree 1.13.2
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++ update rd of `facet_plot` by adding description and example (2018-07-19, Thu)
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 + order by y in `facet_plot` (2018-07-09, Mon)
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 + `extend` parameter in `geom_cladelabel` and `geom_strip` supports specifying
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   extension of both sides (2018-07-06, Fri)
R/facet_plot.R
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@@ -1,6 +1,9 @@
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 ##' plot tree associated data in an additional panel
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 ##'
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 ##'
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+##' 'facet_plot()' automatically re-arranges the input 'data' according to the tree structure,
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+##' visualizes the 'data' on specific 'panel' using the 'geom' function with aesthetic 'mapping' and other parameters,
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+##' and align the graph with the tree 'p' side by side.
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 ##' @title facet_plot
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 ##' @param p tree view
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 ##' @param panel panel name for plot of input data
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@@ -9,6 +12,11 @@
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 ##' @param mapping aes mapping for 'geom'
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 ##' @param ... additional parameters for 'geom'
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 ##' @return ggplot object
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+##' @examples
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+##' tr <- rtree(10)
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+##' dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))
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+##' p <- ggtree(tr)
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+##' facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))
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 ##' @export
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 ##' @author Guangchuang Yu
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 facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {
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@@ -20,7 +28,7 @@ facet_plot <- function(p, panel, data, geom, mapping=NULL, ...) {
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 ##' @importFrom ggplot2 facet_grid
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 add_panel <- function(p, panel) {
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     df <- p$data
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-    if (is.null(df$.panel)) {
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+    if (is.null(df[[".panel"]])) {
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         df[[".panel"]] <- factor("Tree")
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     }
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     levels(df$.panel) %<>% c(., panel)
R/gheatmap.R
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@@ -82,7 +82,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
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     dd$x <- V2
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     dd$width <- width
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-
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+    dd[[".panel"]] <- factor("Tree")
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     if (is.null(color)) {
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         p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, inherit.aes=FALSE)
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     } else {
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@@ -101,6 +101,7 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
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             y <- max(p$data$y) + 1
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         }
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         mapping$y <- y
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+        mapping[[".panel"]] <- factor("Tree")
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         p2 <- p2 + geom_text(data=mapping, aes(x=to, y = y, label=from), size=font.size, inherit.aes = FALSE,
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                              angle=colnames_angle, nudge_x=colnames_offset_x, nudge_y = colnames_offset_y, hjust=hjust)
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     }
README.md
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 <img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" />
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-[![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)
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+[![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)
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-[![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)
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+[![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)
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 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.
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@@ -25,7 +25,7 @@ Please cite the following article when using `ggtree`:
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 **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.
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-[![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)
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+[![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)
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 ------------------------------------------------------------------------
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@@ -35,7 +35,7 @@ Please cite the following article when using `ggtree`:
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 ### Download stats
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-[![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)
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+[![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)
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 <img src="https://guangchuangyu.github.io/software/ggtree/index_files/figure-html/dlstats-1.png" width="890"/>
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man/facet_plot.Rd
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@@ -25,6 +25,17 @@ ggplot object
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 \description{
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 plot tree associated data in an additional panel
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 }
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+\details{
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+'facet_plot()' automatically re-arranges the input 'data' according to the tree structure,
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+visualizes the 'data' on specific 'panel' using the 'geom' function with aesthetic 'mapping' and other parameters,
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+and align the graph with the tree 'p' side by side.
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+}
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+\examples{
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+tr <- rtree(10)
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+dd = data.frame(id=tr$tip.label, value=abs(rnorm(10)))
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+p <- ggtree(tr)
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+facet_plot(p, 'Trait', data = dd, geom=geom_point, mapping=aes(x=value))
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+}
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 \author{
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 Guangchuang Yu
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 }