## ##' @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()
## }
## )
