R/plot_phylo.R
In phylotastic/datelifeplot: Methods to plot chronograms
Defines functions
plot_phylo
Documented in
plot_phylo
#' @import utils
utils::globalVariables(c("strat2012"))
#' Plot a single chronogram with a title and a geochronological axis
#'
#' @details [plot_phylo()] uses different plotting functions to generate a plot
#' of a given chronogram with a time axis representing geologic time.
#'
#' @param chronogram A chronogram either as a newick character string or as a
#' `phylo` object with branch length proportional to time.
#' @param title A character string providing the title for the plot.
#' @param time_depth A numeric vector indicating the upper limit for the time scale on the x axis.
#' @param plot_type A character vector of length one indicating the type of
#' plot to generate. Options are:
#' \describe{
#' \item{"ape"}{It uses the functions [ape::plot.phylo()] and [ape::axisPhylo()].}
#' \item{"phyloch"}{It uses the functions [ape::plot.phylo()] and [phyloch::axisGeo()].}
#' \item{"strap"}{It uses the function [strap::geoscalePhylo()] from the package [strap].}
#' \item{"phytools"}{Not implemented yet. It will use functions from the package [phytools]}
#' }
#' @param time_axis Default to `TRUE`, add a time axis to the tree plot.
#' @param mai1,mai2,mai3,mai4 A numeric value indicating internal plot margin sizes
#' in inches. `mai4` is particularly important as it indicates the space needed for
#' plotting whole tip labels on the right margin of the plot.
#' @param omi1,omi2,omi3,omi4 A numeric value indicating outter plot margin sizes in inches.
#' @param plot_height,plot_width A numeric value indicating height and width for the plot.
#' @param write A character vector of length 1 indicating the file extension to
#' write the plots to. Options are "pdf" or "png". Anything else will not write a file.
#' @param file_name A character string giving the name and path to write the files to.
#' @param geologic_timescale A dataframe of geochronological limits.
#' @param geologic_unit A character vector used to select geological time units that shall be displayed. When using \code{gradstein04}, \code{"eon"}, \code{"era"}, \code{"period"}, \code{"epoch"}, and \code{"stage"} are available.
#' @param cex_axis A numeric indicating character expansion for the axis. Default to value given by `graphics::par("cex")`.
#' @param cex_title A numeric indicating character expansion for the title. Default to value given by `graphics::par("cex")`.
#' @param cex_axislabel A numeric indicating character expansion for the time axis label. Default to value given by `graphics::par("cex")`.
#' @param pos_title Indicates the line position of the title. Default to 1.
#' @param pos_axis Indicates the line position of the axis. Default to 1.
#' @param center_axislabel A numeric indicating centering position of time axis label. Default to 0.5.
#' @param axis_label A character string used to provide information on time units. Defaults
#' to "Time (MYA)" (time in million years ago). If NULL, time units are not added.
#' @param cex_tiplabels A numeric value indicating **c**haracter **ex**pansion (i.e.,
#' size scaling factor) of tip labels in `chronogram`. Default to value given by `graphics::par("cex")`.
#' @inheritParams phyloch::axisGeo
#' @inheritDotParams ape::plot.phylo
#' @importFrom ape .PlotPhyloEnv
#' @export
# enhance: examples of axis_types!
plot_phylo <- function(chronogram,
title = "Chronogram",
time_depth = NULL,
plot_type = "phyloch",
time_axis = TRUE,
mai1, mai2, mai3, mai4,
omi1, omi2, omi3, omi4,
plot_height, plot_width,
write = "no",
file_name = NULL,
geologic_timescale = "strat2012",
geologic_unit = "period",
axis_label = "Time (MYA)",
cex_tiplabels = graphics::par("cex"), # inherits param from plot_node_ages
cex_axislabel = graphics::par("cex"),
cex_axis = graphics::par("cex"),
cex_title = graphics::par("cex"),
pos_title = 1,
pos_axis = 1,
center_axislabel = 0.5,
#pos_axislabel = ,
...){
#
if (!inherits(chronogram, "phylo")) {
if (inherits(chronogram, "multiPhylo")) {
message("'chronogram' is a 'multiPhylo' object. Only first chronogram will be plotted.")
chronogram <- chronogram[[1]]
} else {
message("'chronogram' must be a 'phylo' or 'multiPhylo' object.")
return(NA)
}
}
if (is.null(chronogram$edge.length)) {
message("'chronogram' has no edge lengths; a geologic time axis can not be plotted.")
return(NA)
}
phylo_length <- max(ape::branching.times(chronogram))
if (is.null(time_depth)) {
if (is.null(chronogram$root.edge)) {
time_depth <- round(phylo_length*1.2, digits = -1)
} else {
time_depth <- round(phylo_length + chronogram$root.edge, digits = -1)
}
}
############################################################################
############################################################################
# define plot type
############################################################################
############################################################################
match.arg(arg = plot_type, choices = c("phyloch", "strap", "phytools", "ape"))
if (is.null(geologic_timescale) | "strat2012" %in% geologic_timescale) {
utils::data("strat2012", package = "phyloch")
geologic_timescale <- strat2012
}
############################################################################
############################################################################
# define plot area margins
############################################################################
############################################################################
if (missing(mai1)) {
mai1 <- 0
}
if (missing(mai2)) {
mai2 <- 0
}
if (missing(mai3)) {
mai3 <- 0
}
ind <- which.max(nchar(chronogram$tip.label))
mai4_in <- graphics::strwidth(s = chronogram$tip.label[ind],
units = "inches",
cex = cex_tiplabels,
font = 3)
message("Recommended 'mai4' is ", mai4_in)
if (missing(mai4)) {
mai4 <- mai4_in
}
message("Inner margins applied are mai1 = ", mai1,
", mai2 = ", mai2,
", mai3 = ", mai3,
", mai4 = ", mai4)
pho <- phylo_height_omi(phy = chronogram)
message("Recommended plot area height is ", pho$height)
if (missing(plot_height)) {
plot_height <- pho$height
}
message("Used plot area height' is ", plot_height)
if (missing(omi1)) {
omi1 <- pho$omi1
}
if (missing(omi2)) {
omi2 <- 0
}
if (missing(omi3)) {
omi3 <- 1
}
if (missing(omi4)) {
omi4 <- 0
}
message("Outer margins applied are omi1 = ", omi1,
", omi2 = ", omi2,
", omi3 = ", omi3,
", omi4 = ", omi4)
if (missing(plot_width)) {
plot_width <- 500
}
message("Used plot area width' is ", plot_width)
if ("png" %in% write) {
grDevices::png(file = file_name, height = plot_height, width = plot_width)
}
if ("pdf" %in% write) {
print(plot_height)
grDevices::pdf(file = file_name, height = plot_height/72, width = plot_width/72)
}
graphics::par(xpd = NA,
mai = c(mai1, mai2, mai3, mai4),
omi = c(omi1, omi2, omi3, omi4))
# plot_chronogram.phylo(chronograms[[i]], cex = 1.5, edge.width = 2, label.offset = 0.5,
# x.lim = c(0, max_depth), root.edge = TRUE, root.edge.color = "white")
# graphics::par(xpd = FALSE)
if (plot_type %in% c("ape", "phyloch")) {
ape::plot.phylo(chronogram,
cex = cex_tiplabels, #edge.width = 2,
label.offset = 0.5,
x.lim = c(0, time_depth),
root.edge = TRUE,
plot = TRUE, ...) #
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
if(time_axis) {
if ("ape" %in% plot_type) {
# TODO: fix axis not plotting all the way through the root
# See issue https://github.com/phylotastic/datelifeplot/issues/1
ape::axisPhylo(side = 1, line = pos_axis, cex.axis = cex_axis)
axisChrono(side = 1, unit = NULL, line = pos_axis, cex.axis = cex_axis)
} else { # if ("phyloch" %in% plot_type) {
axisGeo(GTS = geologic_timescale,
unit = geologic_unit,
col = c("gray80", "white"),
gridcol = c("gray80", "white"),
cex = cex_axis,
gridty = "twodash")
}
}
# center_axislabel <- 0.5
}
if ("phytools" %in% plot_type) {
# TODO
message("Plotting a geologic time axis with phytools is not supported yet.")
}
if ("strap" %in% plot_type) {
chronogram$root.time <- phylo_length
strap::geoscalePhylo(tree = chronogram,
x.lim = c(0, phylo_length),
cex.tip = 0.7,
cex.ts = 0.7,
cex.age = 0.7,
width = 4,
tick.scale = 15,
# create boxes using the smallest geologic unit in argument "geologic_unit":
boxes = geologic_unit[length(geologic_unit)],
erotate = 90,
quat.rm = TRUE,
units = axis_label)
# center_axislabel <- 1
}
# add a label to the axis
if (time_axis & !is.null(units)) {
graphics::mtext(axis_label,
cex = cex_axislabel,
side = 1,
font = 2,
line = (omi1-0.2)/0.2,
outer = FALSE,
at = max(lastPP$xx) * center_axislabel # centering of the time axis label
)
}
# add a title to the plot
if (!is.null(title)) {
titlei <- wrap_string_to_plot(string = title, max_cex = cex_title, whole = FALSE)
graphics::mtext(text = titlei$wrapped, outer = TRUE,
cex = titlei$string_cex, font = titlei$string_font, line = pos_title)
}
if (any(c("png", "pdf") %in% write)) {
grDevices::dev.off()
}
}
# chronogram <- plant_bold_otol_tree
# plot_phylo_gg <- function(chronogram, title = "Tree", time_depth = NULL, plot_type = 1,
# cex = graphics::par("cex"), mai4 = NULL, write = "nothing", file_name = NULL, GTS = utils::getAnywhere("strat2012")){
# max_age <- max(ape::branching.times(chronogram))
# age_lim <- max_age*1.2
# grDevices::pdf("test.pdf")
# p <- ggtree::ggtree(chronogram) + ggtree::geom_tiplab() + #ggplot2::xlim(age_lim*0.1,-age_lim) +
# ggplot2::coord_cartesian(xlim = c(age_lim*0.5,-age_lim), ylim = c(-1, ape::Ntip(chronogram)), expand = FALSE) +
# ggplot2::scale_x_continuous(breaks=seq(-age_lim,0,100), labels=abs(seq(-age_lim,0,100))) +
# ggtree::theme_tree2()
# p <- ggtree::revts(p)
# deeptime::gggeo_scale(p, neg = TRUE)
# print(p)
# grDevices::dev.off()
# }
# .PlotPhyloEnv <- new.env()
phylotastic/datelifeplot documentation built on July 14, 2022, 12:35 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions plot_phylo
Documented in plot_phylo
#' @import utils
utils::globalVariables(c("strat2012"))
#' Plot a single chronogram with a title and a geochronological axis
#'
#' @details [plot_phylo()] uses different plotting functions to generate a plot
#' of a given chronogram with a time axis representing geologic time.
#'
#' @param chronogram A chronogram either as a newick character string or as a
#' `phylo` object with branch length proportional to time.
#' @param title A character string providing the title for the plot.
#' @param time_depth A numeric vector indicating the upper limit for the time scale on the x axis.
#' @param plot_type A character vector of length one indicating the type of
#' plot to generate. Options are:
#' \describe{
#' \item{"ape"}{It uses the functions [ape::plot.phylo()] and [ape::axisPhylo()].}
#' \item{"phyloch"}{It uses the functions [ape::plot.phylo()] and [phyloch::axisGeo()].}
#' \item{"strap"}{It uses the function [strap::geoscalePhylo()] from the package [strap].}
#' \item{"phytools"}{Not implemented yet. It will use functions from the package [phytools]}
#' }
#' @param time_axis Default to `TRUE`, add a time axis to the tree plot.
#' @param mai1,mai2,mai3,mai4 A numeric value indicating internal plot margin sizes
#' in inches. `mai4` is particularly important as it indicates the space needed for
#' plotting whole tip labels on the right margin of the plot.
#' @param omi1,omi2,omi3,omi4 A numeric value indicating outter plot margin sizes in inches.
#' @param plot_height,plot_width A numeric value indicating height and width for the plot.
#' @param write A character vector of length 1 indicating the file extension to
#' write the plots to. Options are "pdf" or "png". Anything else will not write a file.
#' @param file_name A character string giving the name and path to write the files to.
#' @param geologic_timescale A dataframe of geochronological limits.
#' @param geologic_unit A character vector used to select geological time units that shall be displayed. When using \code{gradstein04}, \code{"eon"}, \code{"era"}, \code{"period"}, \code{"epoch"}, and \code{"stage"} are available.
#' @param cex_axis A numeric indicating character expansion for the axis. Default to value given by `graphics::par("cex")`.
#' @param cex_title A numeric indicating character expansion for the title. Default to value given by `graphics::par("cex")`.
#' @param cex_axislabel A numeric indicating character expansion for the time axis label. Default to value given by `graphics::par("cex")`.
#' @param pos_title Indicates the line position of the title. Default to 1.
#' @param pos_axis Indicates the line position of the axis. Default to 1.
#' @param center_axislabel A numeric indicating centering position of time axis label. Default to 0.5.
#' @param axis_label A character string used to provide information on time units. Defaults
#' to "Time (MYA)" (time in million years ago). If NULL, time units are not added.
#' @param cex_tiplabels A numeric value indicating **c**haracter **ex**pansion (i.e.,
#' size scaling factor) of tip labels in `chronogram`. Default to value given by `graphics::par("cex")`.
#' @inheritParams phyloch::axisGeo
#' @inheritDotParams ape::plot.phylo
#' @importFrom ape .PlotPhyloEnv
#' @export
# enhance: examples of axis_types!
plot_phylo <- function(chronogram,
title = "Chronogram",
time_depth = NULL,
plot_type = "phyloch",
time_axis = TRUE,
mai1, mai2, mai3, mai4,
omi1, omi2, omi3, omi4,
plot_height, plot_width,
write = "no",
file_name = NULL,
geologic_timescale = "strat2012",
geologic_unit = "period",
axis_label = "Time (MYA)",
cex_tiplabels = graphics::par("cex"), # inherits param from plot_node_ages
cex_axislabel = graphics::par("cex"),
cex_axis = graphics::par("cex"),
cex_title = graphics::par("cex"),
pos_title = 1,
pos_axis = 1,
center_axislabel = 0.5,
#pos_axislabel = ,
...){
#
if (!inherits(chronogram, "phylo")) {
if (inherits(chronogram, "multiPhylo")) {
message("'chronogram' is a 'multiPhylo' object. Only first chronogram will be plotted.")
chronogram <- chronogram[[1]]
} else {
message("'chronogram' must be a 'phylo' or 'multiPhylo' object.")
return(NA)
}
}
if (is.null(chronogram$edge.length)) {
message("'chronogram' has no edge lengths; a geologic time axis can not be plotted.")
return(NA)
}
phylo_length <- max(ape::branching.times(chronogram))
if (is.null(time_depth)) {
if (is.null(chronogram$root.edge)) {
time_depth <- round(phylo_length*1.2, digits = -1)
} else {
time_depth <- round(phylo_length + chronogram$root.edge, digits = -1)
}
}
############################################################################
############################################################################
# define plot type
############################################################################
############################################################################
match.arg(arg = plot_type, choices = c("phyloch", "strap", "phytools", "ape"))
if (is.null(geologic_timescale) | "strat2012" %in% geologic_timescale) {
utils::data("strat2012", package = "phyloch")
geologic_timescale <- strat2012
}
############################################################################
############################################################################
# define plot area margins
############################################################################
############################################################################
if (missing(mai1)) {
mai1 <- 0
}
if (missing(mai2)) {
mai2 <- 0
}
if (missing(mai3)) {
mai3 <- 0
}
ind <- which.max(nchar(chronogram$tip.label))
mai4_in <- graphics::strwidth(s = chronogram$tip.label[ind],
units = "inches",
cex = cex_tiplabels,
font = 3)
message("Recommended 'mai4' is ", mai4_in)
if (missing(mai4)) {
mai4 <- mai4_in
}
message("Inner margins applied are mai1 = ", mai1,
", mai2 = ", mai2,
", mai3 = ", mai3,
", mai4 = ", mai4)
pho <- phylo_height_omi(phy = chronogram)
message("Recommended plot area height is ", pho$height)
if (missing(plot_height)) {
plot_height <- pho$height
}
message("Used plot area height' is ", plot_height)
if (missing(omi1)) {
omi1 <- pho$omi1
}
if (missing(omi2)) {
omi2 <- 0
}
if (missing(omi3)) {
omi3 <- 1
}
if (missing(omi4)) {
omi4 <- 0
}
message("Outer margins applied are omi1 = ", omi1,
", omi2 = ", omi2,
", omi3 = ", omi3,
", omi4 = ", omi4)
if (missing(plot_width)) {
plot_width <- 500
}
message("Used plot area width' is ", plot_width)
if ("png" %in% write) {
grDevices::png(file = file_name, height = plot_height, width = plot_width)
}
if ("pdf" %in% write) {
print(plot_height)
grDevices::pdf(file = file_name, height = plot_height/72, width = plot_width/72)
}
graphics::par(xpd = NA,
mai = c(mai1, mai2, mai3, mai4),
omi = c(omi1, omi2, omi3, omi4))
# plot_chronogram.phylo(chronograms[[i]], cex = 1.5, edge.width = 2, label.offset = 0.5,
# x.lim = c(0, max_depth), root.edge = TRUE, root.edge.color = "white")
# graphics::par(xpd = FALSE)
if (plot_type %in% c("ape", "phyloch")) {
ape::plot.phylo(chronogram,
cex = cex_tiplabels, #edge.width = 2,
label.offset = 0.5,
x.lim = c(0, time_depth),
root.edge = TRUE,
plot = TRUE, ...) #
lastPP <- get("last_plot.phylo", envir = .PlotPhyloEnv)
if(time_axis) {
if ("ape" %in% plot_type) {
# TODO: fix axis not plotting all the way through the root
# See issue https://github.com/phylotastic/datelifeplot/issues/1
ape::axisPhylo(side = 1, line = pos_axis, cex.axis = cex_axis)
axisChrono(side = 1, unit = NULL, line = pos_axis, cex.axis = cex_axis)
} else { # if ("phyloch" %in% plot_type) {
axisGeo(GTS = geologic_timescale,
unit = geologic_unit,
col = c("gray80", "white"),
gridcol = c("gray80", "white"),
cex = cex_axis,
gridty = "twodash")
}
}
# center_axislabel <- 0.5
}
if ("phytools" %in% plot_type) {
# TODO
message("Plotting a geologic time axis with phytools is not supported yet.")
}
if ("strap" %in% plot_type) {
chronogram$root.time <- phylo_length
strap::geoscalePhylo(tree = chronogram,
x.lim = c(0, phylo_length),
cex.tip = 0.7,
cex.ts = 0.7,
cex.age = 0.7,
width = 4,
tick.scale = 15,
# create boxes using the smallest geologic unit in argument "geologic_unit":
boxes = geologic_unit[length(geologic_unit)],
erotate = 90,
quat.rm = TRUE,
units = axis_label)
# center_axislabel <- 1
}
# add a label to the axis
if (time_axis & !is.null(units)) {
graphics::mtext(axis_label,
cex = cex_axislabel,
side = 1,
font = 2,
line = (omi1-0.2)/0.2,
outer = FALSE,
at = max(lastPP$xx) * center_axislabel # centering of the time axis label
)
}
# add a title to the plot
if (!is.null(title)) {
titlei <- wrap_string_to_plot(string = title, max_cex = cex_title, whole = FALSE)
graphics::mtext(text = titlei$wrapped, outer = TRUE,
cex = titlei$string_cex, font = titlei$string_font, line = pos_title)
}
if (any(c("png", "pdf") %in% write)) {
grDevices::dev.off()
}
}
# chronogram <- plant_bold_otol_tree
# plot_phylo_gg <- function(chronogram, title = "Tree", time_depth = NULL, plot_type = 1,
# cex = graphics::par("cex"), mai4 = NULL, write = "nothing", file_name = NULL, GTS = utils::getAnywhere("strat2012")){
# max_age <- max(ape::branching.times(chronogram))
# age_lim <- max_age*1.2
# grDevices::pdf("test.pdf")
# p <- ggtree::ggtree(chronogram) + ggtree::geom_tiplab() + #ggplot2::xlim(age_lim*0.1,-age_lim) +
# ggplot2::coord_cartesian(xlim = c(age_lim*0.5,-age_lim), ylim = c(-1, ape::Ntip(chronogram)), expand = FALSE) +
# ggplot2::scale_x_continuous(breaks=seq(-age_lim,0,100), labels=abs(seq(-age_lim,0,100))) +
# ggtree::theme_tree2()
# p <- ggtree::revts(p)
# deeptime::gggeo_scale(p, neg = TRUE)
# print(p)
# grDevices::dev.off()
# }
# .PlotPhyloEnv <- new.env()
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.