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##' plots simultaneously a whole phylogenetic tree and a portion of it.
##'
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##'
##' @title gzoom
##' @param phy phylo object
##' @param focus selected tips
##' @param subtree logical
##' @param widths widths
##' @return a list of ggplot object
##' @importFrom ggplot2 xlim
##' @importFrom ggplot2 scale_color_manual
##' @author ygc
##' @examples
##' require(ape)
##' data(chiroptera)
##' gzoom(chiroptera, grep("Plecotus", chiroptera$tip.label))
gzoom.phylo <- function(phy, focus, subtree=FALSE, widths=c(.3, .7)) {
if (is.character(focus)) {
focus <- which(phy$tip.label %in% focus)
}
group_name <- "focus"
phy <- gfocus(phy, focus, group_name)
foc <- attr(phy, group_name)
## foc should +1 since the group index start from 0
cols <- c("black", "red")[foc+1]
p1 <- ggtree(phy, color=cols)
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subtr <- drop.tip(phy, phy$tip.label[-focus],
subtree=subtree, rooted=TRUE)
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|
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p2 <- ggtree(subtr, color="red") + geom_tiplab(hjust=-0.05)
p2 <- p2 + xlim(0, max(p2$data$x)*1.2)
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multiplot(p1, p2, ncol=2, widths=widths)
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invisible(list(p1=p1, p2=p2))
}
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gzoom.ggtree <- function(tree_view, focus, widths=c(.3, .7), xmax_adjust=0) {
|
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node <- MRCA(tree_view, focus)
cpos <- get_clade_position(tree_view, node)
p2 <- with(cpos, tree_view+
xlim(xmin, xmax+xmax_adjust)+
ylim(ymin, ymax))
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multiplot(tree_view, p2, ncol=2, widths=widths)
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invisible(list(p1=tree_view, p2=p2))
}
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##' @name gzoom
##' @title gzoom method
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##' @rdname gzoom-methods
##' @exportMethod gzoom
##' @param xmax_adjust adjust xmax (xlim[2])
|
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##' @aliases gzoom,ggtree-method
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setMethod("gzoom", signature(object="ggtree"),
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function(object, focus, widths=c(.3, .7), xmax_adjust=0) {
|
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gzoom.ggtree(object, focus, widths, xmax_adjust)
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})
|
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## ##' @rdname gzoom-methods
## ##' @exportMethod gzoom
## setMethod("gzoom", signature(object="apeBootstrap"),
## function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
## gzoom.phylo(get.tree(object), focus, subtree, widths)
## })
|
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|
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## ##' zoom selected subtree
## ##'
## ##'
## ##' @rdname gzoom-methods
## ##' @exportMethod gzoom
## setMethod("gzoom", signature(object="beast"),
## function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
## gzoom.phylo(get.tree(object), focus, subtree, widths)
## })
|
| 3e4b5998 |
|
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## ##' @rdname gzoom-methods
## ##' @exportMethod gzoom
## setMethod("gzoom", signature(object="codeml"),
## function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
## gzoom.phylo(get.tree(object), focus, subtree, widths)
## })
|
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|
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##' zoom selected subtree
##'
##'
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##' @rdname gzoom-methods
##' @exportMethod gzoom
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setMethod("gzoom", signature(object="treedata"),
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function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
gzoom.phylo(get.tree(object), focus, subtree, widths)
})
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## ##' @rdname gzoom-methods
## ##' @exportMethod gzoom
## setMethod("gzoom", signature(object="paml_rst"),
## function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
## gzoom.phylo(get.tree(object), focus, subtree, widths)
## })
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##' @rdname gzoom-methods
##' @exportMethod gzoom
setMethod("gzoom", signature(object="phylo"),
function(object, focus, subtree=FALSE, widths=c(.3, .7)) {
gzoom.phylo(object, focus, subtree, widths)
})
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gfocus <- treeio:::gfocus
|
