1. ggtree
  2. Commit 09d5ff66402c9342e26a1e4909f0883120133d43
Browse code

facet_plot supports ggbio::geom_alignment

guangchuang yu authored on 26/10/2016 08:27:56
Showing 4 changed files
DESCRIPTION
History View file @ 09d5ff66
... ... 
@@ -6,7 +6,8 @@ Authors@R: c(
6 6 
 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),
7 7 
 	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = "ths"),
8 8 
 	   person("Justin", "Silverman", email = "jsilve24@gmail.com", rol = "ctb", comment = "geom_balance"),
9 
-	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb", comment = "propose using txtConnection so that parser functions can use tree strings as input")
9 
+	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb",
10 
+	          comment = "propose using txtConnection so that parser functions can use tree strings as input")
10 11 
 	   )
11 12 
 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
12 13 
 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
NEWS
History View file @ 09d5ff66
... ... 
@@ -1,5 +1,7 @@
1 1 
 CHANGES IN VERSION 1.7.1
2 2 
 ------------------------
3 
+ o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
4 
+   + https://github.com/tengfei/ggbio/issues/83
3 5 
  o make tree stats available in facet_plot <2016-10-24, Mon>
4 6
5 7 
 CHANGES IN VERSION 1.6.0
R/operator.R
History View file @ 09d5ff66
... ... 
@@ -100,10 +100,22 @@
100 100 
 ##' @author Guangchuang Yu
101 101 
 `%+>%` <- function(p, data) {
102 102 
     df <- p$data
103 
-    ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
104 
-    res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE)
105 103 
     lv <- levels(df$panel)
106 
-    res$panel <- factor(lv[length(lv)], levels=lv)
104 
+
105 
+    if (is(data, "GRanges") || is(data, "GRangesList")) {
106 
+        names(data) <- df$y[match(names(data), df$label)]
107 
+        res <- data[order(as.numeric(names(data)))]
108 
+        mcols <- get_fun_from_pkg("GenomicRanges", "mcols")
109 
+        `mcols<-` <- get_fun_from_pkg("GenomicRanges", "`mcols<-`")
110 
+        mcols(res)$panel <- factor(lv[length(lv)], levels=lv)
111 
+    } else if (is(data, "data.frame") || is(data, "tbl_df")) {
112 
+        data <- as.data.frame(data)
113 
+        ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
114 
+        res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE)
115 
+        res$panel <- factor(lv[length(lv)], levels=lv)
116 
+    } else {
117 
+        stop("input 'data' is not supported...")
118 
+    }
107 119 
     return(res)
108 120 
 }
109 121
README.md
History View file @ 09d5ff66
... ... 
@@ -1,9 +1,9 @@
1 1 
 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
2 2 
 ===========================================================================================================================
3 3
4 
-[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.0-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.1-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) [![total](https://img.shields.io/badge/downloads-15614/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
4 
+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.1-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) [![total](https://img.shields.io/badge/downloads-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
5 5
6 
-[![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-2016--10--25-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)
6 
+[![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-2016--10--26-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)
7 7
8 8 
 [![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)
9 9
... ... 
@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
50 50
51 51 
 ### Download stats
52 52
53 
-[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-15614/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
53 
+[![download](http://www.bioconductor.org/shields/downloads/ggtree.svg)](https://bioconductor.org/packages/stats/bioc/ggtree/) [![total](https://img.shields.io/badge/downloads-15734/total-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree) [![month](https://img.shields.io/badge/downloads-1678/month-blue.svg?style=flat)](https://bioconductor.org/packages/stats/bioc/ggtree)
54 54
55 55 
          +-------------------------+------------------------+-------------------------+----------------+
56 56 
          |                                                                                         *   |