1. ggtree
  2. Commit 9cbaf87bb99d0b6f2d2cbc95abbcc49a25ad660d
Browse code

subset supports logical vector contains NA, and geom_cladelabel supports parsing emoji

guangchuang yu authored on 16/02/2017 06:10:17
Showing 7 changed files
NEWS
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@@ -1,9 +1,11 @@
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 CHANGES IN VERSION 1.7.7
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 ------------------------
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+ o geom_cladelabel support parse="emoji" <2017-02-16, Thu>
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+ o aes(subset) now support logical vector contains NA <2017-02-16, Thu>
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  o add legend transparency to theme_transparent <2017-02-13, Mon>
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    + <https://github.com/GuangchuangYu/ggtree/pull/112>
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  o update citation info <2017-01-20, Fri>
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-
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+
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 CHANGES IN VERSION 1.7.6
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 ------------------------
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  o inset support reverse scale <2017-01-05, Thu>
R/geom_cladelabel.R
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@@ -47,6 +47,13 @@ geom_cladelabel <- function(node, label, offset=0, offset.text=0,
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         }
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     }
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+    if (parse == 'emoji') {
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+        emoji <- get_fun_from_pkg("emojifont", "emoji")
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+        label <- emoji(label)
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+        parse <- FALSE
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+        family <- "OpenSansEmoji"
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+    }
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+
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     if (is.null(color)) {
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         if (geom == "text") {
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             ## no fill parameter
R/geom_label.R
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@@ -78,7 +78,7 @@ GeomLabelGGtree <- ggproto("GeomLabelGGtree", GeomLabel,
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                            setup_data = function(data, params) {
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                                if (is.null(data$subset))
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                                    return(data)
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-                               data[data$subset,]
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+                               data[which(data$subset),]
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                            },
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                            draw_panel = function(self, data, panel_scales, coord, parse = FALSE,
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                                                  na.rm = FALSE,
R/geom_point.R
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@@ -137,7 +137,7 @@ GeomPointGGtree <- ggproto("GeomPointGGtree", GeomPoint,
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                            setup_data = function(data, params) {
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                                if (is.null(data$subset))
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                                    return(data)
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-                               data[data$subset,]
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+                               data[which(data$subset),]
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                            }
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                            ## ,
R/geom_segment.R
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@@ -78,7 +78,7 @@ GeomSegmentGGtree <- ggproto("GeomSegmentGGtree", GeomSegment,
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                              setup_data = function(data, params) {
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                                  if (is.null(data$subset))
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                                      return(data)
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-                                 data[data$subset,]
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+                                 data[which(data$subset),]
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                              },
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                              draw_panel = function(data, panel_scales, coord, arrow = NULL,
R/geom_text.R
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@@ -66,7 +66,7 @@ GeomTextGGtree <- ggproto("GeomTextGGtree", GeomText,
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                           setup_data = function(data, params) {
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                               if (is.null(data$subset))
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                                   return(data)
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-                              data[data$subset,]
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+                              data[which(data$subset),] ## use `which` makes it compatible with NA
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                           },
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                           ## compute_group = function(data, params) {
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                           ##     data
README.md
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@@ -4,7 +4,7 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with
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 [![releaseVersion](https://img.shields.io/badge/release%20version-1.6.9-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.7-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-21822/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1894/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) <img src="logo.png" align="right" />
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-[![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-2017--02--15-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)
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+[![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-2017--02--16-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)
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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) [![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)
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@@ -18,7 +18,7 @@ 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) [![citation](https://img.shields.io/badge/cited%20by-7-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-345-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) [![citation](https://img.shields.io/badge/cited%20by-7-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-351-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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