git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@123745 bc3139a8-67e5-0310-9ffc-ced21a209358
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1 | 1 |
Package: ggtree |
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Type: Package |
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Title: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data |
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-Version: 1.7.2 |
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+Version: 1.7.3 |
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5 | 5 |
Authors@R: c( |
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person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre", "cph")), |
7 | 7 |
person("Tommy Tsan-Yuk", "Lam", email = "tylam.tommy@gmail.com", rol = c("aut", "ths")), |
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@@ -1,5 +1,11 @@ |
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+CHANGES IN VERSION 1.7.3 |
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+------------------------ |
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+ o reverse timescale x-axis <2016-11-07, Mon> |
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+ + https://github.com/GuangchuangYu/ggtree/issues/87 |
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+ |
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CHANGES IN VERSION 1.7.2 |
2 | 7 |
------------------------ |
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+ o make missing colors in gheatmap invisible (previously use 'white') <2016-11-03, Thu> |
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3 | 9 |
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') |
5 | 11 |
o bug fixed of parsing tree text in beast file <2016-10-31, Mon> |
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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$value,"numeric")) { |
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- p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value="white") |
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+ p2 <- p2 + scale_fill_gradient(low=low, high=high, na.value=NA) # "white") |
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} else { |
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- p2 <- p2 + scale_fill_discrete(na.value="white") |
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+ p2 <- p2 + scale_fill_discrete(na.value=NA) #"white") |
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} |
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if (colnames) { |
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@@ -26,3 +26,17 @@ xlim_expand <- function(xlim, panel) { |
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geom_blank(aes_(x=~x), dummy, inherit.aes = FALSE) |
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} |
28 | 28 |
|
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+##' reverse timescle x-axis |
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+##' |
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+##' |
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+##' @title revts |
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+##' @param treeview treeview |
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+##' @return updated treeview |
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+##' @export |
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+##' @author guangchuang yu |
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+revts <- function(treeview) { |
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+ x <- treeview$data$x |
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+ x <- x - max(x) |
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+ treeview$data$x <- x |
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+ treeview |
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+} |
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@@ -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 |
|
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-[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
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+[](https://bioconductor.org/packages/ggtree) [](https://github.com/GuangchuangYu/ggtree) [](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#since) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
|
5 | 5 |
|
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-[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
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+[](http://www.repostatus.org/#active) [](https://codecov.io/gh/GuangchuangYu/ggtree) [](https://github.com/GuangchuangYu/ggtree/commits/master) [](https://github.com/GuangchuangYu/ggtree/network) [](https://github.com/GuangchuangYu/ggtree/stargazers) [](https://awesome-r.com/#awesome-r-graphic-displays) |
|
7 | 7 |
|
8 | 8 |
[](https://www.bioconductor.org/packages/devel/bioc/html/ggtree.html#archives) [](https://bioconductor.org/checkResults/devel/bioc-LATEST/ggtree/) [](https://travis-ci.org/GuangchuangYu/ggtree) [](https://ci.appveyor.com/project/GuangchuangYu/ggtree) [](http://bioconda.github.io/recipes/bioconductor-ggtree/README.html) |
9 | 9 |
|
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@@ -17,7 +17,7 @@ Please cite the following article when using `ggtree`: |
17 | 17 |
|
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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* |
19 | 19 |
|
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-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
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+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) [](https://www.altmetric.com/details/10533079) |
|
21 | 21 |
|
22 | 22 |
------------------------------------------------------------------------ |
23 | 23 |
|
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@@ -50,30 +50,30 @@ For details, please visit our project website, <https://guangchuangyu.github.io/ |
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|
51 | 51 |
### Download stats |
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-[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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+[](https://bioconductor.org/packages/stats/bioc/ggtree/) [](https://bioconductor.org/packages/stats/bioc/ggtree) [](https://bioconductor.org/packages/stats/bioc/ggtree) |
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- +-------------------------+------------------------+-------------------------+----------------+ |
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+ +------------------------+-----------------------+-----------------------+--------------------+ |
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+ | * | |
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1500 + + |
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- | * * | |
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+ | * | |
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+ | * * | |
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+ | * * * | |
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1000 + + |
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- 500 + * + |
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- 0 + * * * + |
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- +-------------------------+------------------------+-------------------------+----------------+ |
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- 2015 2015.5 2016 2016.5 |
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+ 0 + * * * + |
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+ +------------------------+-----------------------+-----------------------+--------------------+ |
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+ 2015 2015.5 2016 2016.5 |
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new file mode 100644 |
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@@ -0,0 +1,21 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/xlim.R |
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+\name{revts} |
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+\alias{revts} |
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+\title{revts} |
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+\usage{ |
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+revts(treeview) |
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+} |
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+\arguments{ |
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+\item{treeview}{treeview} |
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+} |
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+\value{ |
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+updated treeview |
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+} |
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+\description{ |
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+reverse timescle x-axis |
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+} |
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+\author{ |
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+guangchuang yu |
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+} |
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+ |