git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/ggtree@118985 bc3139a8-67e5-0310-9ffc-ced21a209358
Guangchuang Yu authored on 28/06/2016 06:26:04
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@@ -20,6 +20,7 @@ S3method(fortify,phylo4d) |
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S3method(fortify,phyloseq) |
| 21 | 21 |
S3method(fortify,r8s) |
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S3method(fortify,raxml) |
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+S3method(identify,gg) |
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S3method(print,beastList) |
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export("%<%")
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export("%<+%")
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@@ -215,7 +216,12 @@ importFrom(ggplot2,ylab) |
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importFrom(grDevices,col2rgb) |
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importFrom(grDevices,colorRampPalette) |
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importFrom(grDevices,rgb) |
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+importFrom(graphics,identify) |
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+importFrom(grid,convertX) |
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+importFrom(grid,convertY) |
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+importFrom(grid,dataViewport) |
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importFrom(grid,grid.layout) |
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+importFrom(grid,grid.locator) |
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importFrom(grid,grid.newpage) |
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importFrom(grid,pushViewport) |
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importFrom(grid,rasterGrob) |
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@@ -43,7 +43,7 @@ ggtree <- function(tr, |
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branch.length = "branch.length", |
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ndigits = NULL, |
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...) {
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- |
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+ |
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layout %<>% match.arg(c("rectangular", "slanted", "fan", "circular", "radial", "unrooted"))
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| 48 | 48 |
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if (is(tr, "r8s") && branch.length == "branch.length") {
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@@ -90,6 +90,6 @@ ggtree <- function(tr, |
| 90 | 90 |
} else if (layout == "fan") {
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p <- layout_fan(p, open.angle) |
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} |
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- |
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+ |
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return(p) |
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} |
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new file mode 100644 |
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@@ -0,0 +1,37 @@ |
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+ |
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+##' identify node by interactive click |
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+##' |
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+##' |
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+##' @rdname identify |
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+##' @title identify |
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+##' @param x tree view |
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+##' @param ... additional parameters |
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+##' @return node id |
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+##' @importFrom grid convertX |
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+##' @importFrom grid convertY |
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+##' @importFrom grid pushViewport |
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+##' @importFrom grid grid.locator |
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+##' @importFrom grid unit |
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+##' @importFrom grid dataViewport |
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+##' @importFrom graphics identify |
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+##' @method identify gg |
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+##' @export |
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+##' @author Guangchuang Yu |
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+identify.gg <- function(x, ...) {
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+ tree_view <- x |
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+ ## not used, since if x=NULL, it will call graphics::identify |
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+ ## tree_view %<>% get_tree_view |
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+ |
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+ x <- tree_view$data$x |
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+ y <- tree_view$data$y |
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+ |
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+ pushViewport(dataViewport(x, y)) |
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+ loc <- grid.locator('in') %>% as.numeric
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+ |
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+ xx <- as.numeric(convertX( unit(x,'native'), 'in' )) |
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+ yy <- as.numeric(convertY( unit(y,'native'), 'in' )) |
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+ |
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+ idx <- which.min( (xx-loc[1])^2 + (yy-loc[2])^2 ) |
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+ return(tree_view$data$node[idx]) |
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+} |
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+ |
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new file mode 100644 |
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@@ -0,0 +1,23 @@ |
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+% Generated by roxygen2: do not edit by hand |
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+% Please edit documentation in R/method-identify.R |
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+\name{identify.gg}
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+\alias{identify.gg}
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+\title{identify}
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+\usage{
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+\method{identify}{gg}(x, ...)
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+} |
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+\arguments{
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+\item{x}{tree view}
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+ |
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+\item{...}{additional parameters}
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+} |
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+\value{
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+node id |
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+} |
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+\description{
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+identify node by interactive click |
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+} |
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+\author{
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+Guangchuang Yu |
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+} |
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+ |