1. ggtree
  2. Commit 39aaccd58c8fdbbc4ba8f6500bcaa2782628f736
Browse code

make missing color invisible

GuangchuangYu authored on 03/11/2016 15:30:13
Showing3 changed files
  • NEWS index 9e9525d3..d88839ae 100644
  • R/gheatmap.R index 379b1c59..7facb2e6 100644
  • README.md index c97c0e28..46e00550 100644
NEWS
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@@ -1,5 +1,6 @@
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 CHANGES IN VERSION 1.7.2
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 ------------------------
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+ o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu>
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  o xlim_expand for setting x axis limits of specific panel <2016-11-01, Tue>
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    + xlim_tree is now a specific case of xlim_expand(xlim, panel='Tree')
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  o bug fixed of parsing tree text in beast file <2016-10-31, Mon>
R/gheatmap.R
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@@ -79,9 +79,9 @@ gheatmap <- function(p, data, offset=0, width=1, low="green", high="red", color=
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         p2 <- p + geom_tile(data=dd, aes(x, y, fill=value), width=width, color=color, inherit.aes=FALSE)
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     }
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     if (is(dd$value,"numeric")) {
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-        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white")
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+        p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA) # "white")
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     } else {
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-        p2 <- p2 + scale_fill_discrete(na.value="white")
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+        p2 <- p2 + scale_fill_discrete(na.value=NA) #"white")
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     }
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     if (colnames) {
README.md
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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-1.6.1-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.2-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) [![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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+[![releaseVersion](https://img.shields.io/badge/release%20version-1.6.2-green.svg?style=flat)](https://bioconductor.org/packages/ggtree) [![develVersion](https://img.shields.io/badge/devel%20version-1.7.2-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) [![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--11--01-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--11--03-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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