guangchuang yu authored on 22/08/2017 08:22:37
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@@ -43,4 +43,4 @@ BugReports: https://github.com/GuangchuangYu/ggtree/issues |
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Packaged: 2014-12-03 08:16:14 UTC; root |
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biocViews: Alignment, Annotation, Clustering, DataImport, |
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MultipleSequenceAlignment, ReproducibleResearch, Software, Visualization |
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-RoxygenNote: 5.0.1 |
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+RoxygenNote: 6.0.1 |
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@@ -1,5 +1,7 @@ |
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CHANGES IN VERSION 1.9.4 |
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------------------------ |
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+ o geom_motif for aligned motif <2017-08-22, Tue> |
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+ + https://github.com/GuangchuangYu/ggtree/issues/148 |
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o fixed `R CMD build` error: cannot stat 'ggtree/site_src/themes': No such file or directory <2017-08-22, Tue> |
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CHANGES IN VERSION 1.9.3 |
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@@ -1,3 +1,37 @@ |
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+##' geom layer to draw aligned motif |
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+##' |
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+##' |
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+##' @title geom_motif |
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+##' @param mapping aes mapping |
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+##' @param data data |
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+##' @param on gene to center (i.e. set middle position of the `on` gene to 0) |
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+##' @param ... additional parameters |
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+##' @return geom layer |
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+##' @export |
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+##' @author guangchuang yu |
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+geom_motif <- function(mapping, data, on, ...) {
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+ if (is.null(unlist(mapping)$y)) {
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+ seqnames <- as.character(unlist(mapping)$group) |
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+ } else {
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+ seqnames <- as.character(unlist(mapping)$y) |
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+ } |
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+ |
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+ if (is.null(unlist(mapping$fill))) {
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+ id <- as.character(unlist(mapping$id)) |
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+ } else {
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+ id <- as.character(unlist(mapping$fill)) |
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+ } |
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+ dd <- data[unlist(data[, id]) == on,] |
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+ mid <- dd$start + (dd$end - dd$start)/2 |
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+ names(mid) <- as.character(unlist(dd[, seqnames])) |
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+ adj <- mid[as.character(unlist(data[, seqnames]))] |
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+ data$start <- data$start - adj |
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+ data$end <- data$end - adj |
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+ geom_gene_arrow <- get_fun_from_pkg("gggenes", "geom_gene_arrow")
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+ geom_gene_arrow(mapping = mapping, data = as.data.frame(data), ...) |
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+} |
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+ |
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+ |
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plot_fantree <- function(fantree, upper=TRUE) {
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if (upper) {
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ymin <- -.25 |
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@@ -4,9 +4,9 @@ ggtree: an R package for visualization and annotation of phylogenetic trees with |
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<img src="https://raw.githubusercontent.com/Bioconductor/BiocStickers/master/ggtree/ggtree.png" height="200" align="right" /> |
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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) |
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| 8 | 8 |
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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) |
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| 10 | 10 |
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[](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) [](#backers) [](#sponsors) |
| 12 | 12 |
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@@ -27,7 +27,7 @@ Please cite the following article when using `ggtree`: |
| 27 | 27 |
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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. |
| 29 | 29 |
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-[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
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+[](http://dx.doi.org/10.1111/2041-210X.12628) [](https://www.altmetric.com/details/10533079) [](https://scholar.google.com.hk/scholar?oi=bibs&hl=en&cites=7268358477862164627) |
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| 31 | 31 |
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------------------------------------------------------------------------ |
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|
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@@ -37,7 +37,7 @@ Please cite the following article when using `ggtree`: |
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### 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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<img src="docs/images/dlstats.png" width="890"/> |
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@@ -30,11 +30,10 @@ highlights the two direct descendant clades of an internal node |
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Particularly useful when studying neighboring clades. Note that balances that |
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correspond to multichotomies will not be displayed. |
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} |
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-\author{
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-Justin Silverman |
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-} |
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\references{
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J. Silverman, et al. \emph{A phylogenetic transform enhances
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analysis of compositional microbiota data}. (in preparation) |
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} |
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- |
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+\author{
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+Justin Silverman |
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+} |
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new file mode 100644 |
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@@ -0,0 +1,26 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/experimental_function.R |
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+\name{geom_motif}
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+\alias{geom_motif}
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+\title{geom_motif}
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+\usage{
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+geom_motif(mapping, data, on, ...) |
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+} |
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+\arguments{
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+\item{mapping}{aes mapping}
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+ |
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+\item{data}{data}
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+ |
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+\item{on}{gene to center (i.e. set middle position of the `on` gene to 0)}
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+ |
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+\item{...}{additional parameters}
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+} |
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+\value{
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+geom layer |
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+} |
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+\description{
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+geom layer to draw aligned motif |
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+} |
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+\author{
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+guangchuang yu |
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+} |
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@@ -18,4 +18,3 @@ named list of subtrees with the root id of subtree and list of node id's making |
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Get all subtrees of node, as well as remaining branches of parent (ie, rest of tree structure as subtree) |
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return named list of subtrees with list name as starting node id. |
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} |
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- |
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@@ -3,8 +3,9 @@ |
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\docType{package}
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\name{ggtree}
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\alias{ggtree}
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-\alias{ggtree-package}
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\alias{package-ggtree}
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+\alias{ggtree-package}
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+\alias{ggtree}
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\title{visualizing phylogenetic tree and heterogenous associated data based on grammar of graphics
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\code{ggtree} provides functions for visualizing phylogenetic tree and its associated data in R.}
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\usage{
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@@ -57,4 +58,3 @@ ggtree(tr) |
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\author{
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Yu Guangchuang |
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} |
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- |
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@@ -3,12 +3,13 @@ |
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\docType{methods}
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\name{gzoom}
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\alias{gzoom}
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+\alias{gzoom}
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+\alias{gzoom,ggtree-method}
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\alias{gzoom,beast-method}
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\alias{gzoom,codeml-method}
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-\alias{gzoom,ggtree-method}
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+\alias{gzoom,treedata-method}
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\alias{gzoom,paml_rst-method}
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\alias{gzoom,phylo-method}
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-\alias{gzoom,treedata-method}
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\title{gzoom method}
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\usage{
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gzoom(object, focus, subtree = FALSE, widths = c(0.3, 0.7), ...) |
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@@ -50,4 +51,3 @@ figure |
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\description{
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zoom selected subtree |
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} |
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- |
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@@ -4,9 +4,9 @@ |
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\name{scale_color}
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\alias{scale_color}
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\alias{scale_color,beast-method}
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+\alias{scale_color,treedata-method}
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\alias{scale_color,paml_rst-method}
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\alias{scale_color,phylo-method}
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-\alias{scale_color,treedata-method}
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\title{scale_color method}
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\usage{
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scale_color(object, by, ...) |
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@@ -33,4 +33,3 @@ color vector |
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\description{
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scale color by a numerical tree attribute |
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} |
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- |
