1. ggtree
  2. Commit 189e99b242605864ecc92764f14a91f27485df86
Browse code

facet_plot supports ggbio::geom_alignment

git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@123042 bc3139a8-67e5-0310-9ffc-ced21a209358

Guangchuang Yu authored on 26/10/2016 08:28:49
Showing 4 changed files
DESCRIPTION
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@@ -4,12 +4,11 @@ Title: an R package for visualization and annotation of phylogenetic trees with
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 Version: 1.7.1
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 Authors@R: c(
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 	   person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre")),
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-	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = "aut"),
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+	   person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = "ths"),
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 	   person("Justin", "Silverman", email = "jsilve24@gmail.com", rol = "ctb", comment = "geom_balance"),
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-	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb", comment = "propose using txtConnection so that parser functions can use tree strings as input")
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+	   person("Casey", "Dunn", email = "casey_dunn@brown.edu", rol = "ctb",
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+	          comment = "propose using txtConnection so that parser functions can use tree strings as input")
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 	   )
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-Author: Guangchuang Yu <guangchuangyu@gmail.com> and Tommy Tsan-Yuk Lam with contributions from
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-   	Justin Silverman and Casey Dunn.
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 Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
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 Description: 'ggtree' extends the 'ggplot2' plotting system which implemented the grammar of graphics.
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 	     'ggtree' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.
NEWS
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@@ -1,5 +1,7 @@
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 CHANGES IN VERSION 1.7.1
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 ------------------------
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+ o facet_plot supports ggbio::geom_alignment <2016-10-26, Wed>
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+   + https://github.com/tengfei/ggbio/issues/83
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  o make tree stats available in facet_plot <2016-10-24, Mon>
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 CHANGES IN VERSION 1.6.0
R/operator.R
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@@ -100,10 +100,22 @@
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 ##' @author Guangchuang Yu
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 `%+>%` <- function(p, data) {
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     df <- p$data
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-    ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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-    res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE)
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     lv <- levels(df$panel)
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-    res$panel <- factor(lv[length(lv)], levels=lv)
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+
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+    if (is(data, "GRanges") || is(data, "GRangesList")) {
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+        names(data) <- df$y[match(names(data), df$label)]
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+        res <- data[order(as.numeric(names(data)))]
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+        mcols <- get_fun_from_pkg("GenomicRanges", "mcols")
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+        `mcols<-` <- get_fun_from_pkg("GenomicRanges", "`mcols<-`")
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+        mcols(res)$panel <- factor(lv[length(lv)], levels=lv)
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+    } else if (is(data, "data.frame") || is(data, "tbl_df")) {
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+        data <- as.data.frame(data)
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+        ## res <- merge(df[, c('label', 'y')], data, by.x='label', by.y=1) ## , all.x=TRUE)
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+        res <- merge(df, data, by.x='label', by.y=1) ## , all.x=TRUE)
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+        res$panel <- factor(lv[length(lv)], levels=lv)
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+    } else {
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+        stop("input 'data' is not supported...")
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+    }
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     return(res)
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 }
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README.md
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@@ -1,9 +1,9 @@
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 ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data
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 ===========================================================================================================================
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-[![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)
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+[![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)
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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-2016--10--24-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-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)
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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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@@ -17,7 +17,7 @@ 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***. *accepted*
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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-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-246-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-1-green.svg?style=flat)](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [![Altmetric](https://img.shields.io/badge/Altmetric-250-green.svg?style=flat)](https://www.altmetric.com/details/10533079)
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 ------------------------------------------------------------------------
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@@ -50,7 +50,7 @@ For details, please visit our project website, <https://guangchuangyu.github.io/
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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-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)
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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-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)
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          +-------------------------+------------------------+-------------------------+----------------+
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          |                                                                                         *   |