##' @rdname plot-methods
##' @exportMethod plot
##' @param tip.label.size size of tip label
##' @param tip.label.hjust hjust of tip.label
##' @param annotation.size size of annotation
##' @param annotation.color color of annotation
##' @examples
##' file <- system.file("extdata/BEAST", "beast_mcc.tree", package="ggtree")
##' beast <- read.beast(file)
##' plot(beast, annotation="length_0.95_HPD", branch.length="none") + theme_tree()
setMethod("plot", signature( x= "beast"),
function(x, layout = "rectangular",
branch.length = "branch.length",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = -0.1,
position = "branch",
annotation = "rate",
ndigits = 2,
annotation.size = 3,
annotation.color = "black",
...) {
p <- ggtree(x, layout = layout,
branch.length = branch.length,
ndigits = ndigits, ...)
if (show.tip.label) {
p <- p + geom_tiplab(hjust = tip.label.hjust,
size = tip.label.size)
offset <- ceiling(max(p$data$x)) * 0.1
p <- p + xlim(-offset, max(p$data$x) + offset)
}
if (!is.null(annotation) && !is.na(annotation)) {
if (position == "node") {
position <- "x"
vjust <- 0
hjust <- -.05
} else {
vjust <- -.5
hjust <- 0
}
p <- p + geom_text(aes_string(x=position,
label=annotation),
size=annotation.size,
vjust= vjust, hjust = hjust,
color=annotation.color)
}
p + theme_tree2()
})
##' @rdname plot-methods
##' @exportMethod plot
##' @param layout layout
##' @param branch.length branch length
##' @param show.tip.label logical
##' @param position one of "branch" and "node"
##' @param annotation one of get.fields(x)
##' @param ndigits round digits
setMethod("plot", signature(x = "codeml_mlc"),
function(x, layout = "rectangular",
branch.length = "branch.length",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = -0.1,
position = "branch",
annotation = "dN_vs_dS",
annotation.size = 3,
annotation.color = "black",
ndigits = 2,
...
) {
p <- ggtree(x, layout=layout,
branch.length=branch.length,
ndigits=ndigits, ...)
if (show.tip.label) {
p <- p + geom_tiplab(hjust = tip.label.hjust,
size = tip.label.size)
}
plot.codeml_mlc_(p, position, annotation,
annotation.size, annotation.color)
})
##' @rdname plot-methods
##' @exportMethod plot
setMethod("plot", signature( x= "r8s"),
function(x, layout = "rectangular",
branch.length = "TREE",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = 0,
...) {
p <- ggtree(x, layout = layout,
branch.length = branch.length, ...)
if (show.tip.label) {
p <- p + geom_tiplab(hjust = tip.label.hjust,
size = tip.label.size)
offset <- ceiling(max(p$data$x)) * 0.1
p <- p + xlim(NA, max(p$data$x) + offset)
}
p + theme_tree2()
})
##' @rdname plot-methods
##' @exportMethod plot
setMethod("plot", signature( x= "raxml"),
function(x, layout = "rectangular",
branch.length = "branch.length",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = 0,
position = "node",
annotation = "bootstrap",
ndigits = 2,
annotation.size = 4,
annotation.color = "black",
...) {
p <- ggtree(x, layout = layout,
branch.length = branch.length,
ndigits = ndigits, ...)
if (show.tip.label) {
p <- p + geom_tiplab(hjust = tip.label.hjust,
size = tip.label.size)
offset <- ceiling(max(p$data$x)) * 0.1
p <- p + xlim(NA, max(p$data$x) + offset)
}
if (!is.null(annotation) && !is.na(annotation)) {
if (position == "node") {
position <- "x"
vjust <- 0
hjust <- -.05
} else {
vjust <- -.5
hjust <- 0
}
p <- p + geom_text(aes_string(x=position,
label=annotation),
size=annotation.size,
vjust= vjust, hjust = hjust,
color=annotation.color)
}
p + theme_tree2()
})
##' @rdname plot-methods
##' @exportMethod plot
setMethod("plot", signature(x = "paml_rst"),
function(x, layout = "rectangular",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = -0.1,
position = "branch",
annotation = "marginal_subs",
annotation.color = "black",
annotation.size = 3,
...) {
plot.subs(x, layout, show.tip.label,
tip.label.size,
tip.label.hjust,
position, annotation,
annotation.color,
annotation.size, ...)
})
##' @rdname plot-methods
##' @exportMethod plot
setMethod("plot", signature(x = "hyphy"),
function(x, layout = "rectangular",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = -0.1,
position = "branch",
annotation = "subs",
annotation.color = "black",
annotation.size = 3,
...) {
plot.subs(x, layout, show.tip.label,
tip.label.size,
tip.label.hjust,
position, annotation,
annotation.color,
annotation.size,...)
})
##' @rdname plot-methods
##' @exportMethod plot
##' @importFrom ggplot2 aes_string
setMethod("plot", signature(x = "codeml"),
function(x, layout = "rectangular",
branch.length = "mlc.branch.length",
show.tip.label = TRUE,
tip.label.size = 4,
tip.label.hjust = -0.1,
position = "branch",
annotation = "dN_vs_dS",
annotation.size = 3,
annotation.color = "black",
ndigits = 2,
...) {
p <- ggtree(x, layout = layout,
branch.length = branch.length,
ndigits=ndigits, ...)
if (show.tip.label) {
p <- p + geom_tiplab(hjust = tip.label.hjust,
size = tip.label.size)
}
if (!is.null(annotation) && !is.na(annotation)) {
p <- p + geom_text(aes_string(x=position,
label = annotation),
size = annotation.size, vjust = -.5,
color = annotation.color)
}
p + theme_tree2()
}
)
