plot_node_ages: Plot a Chronogram and Add Age Data to Nodes

In phylotastic/datelifeplot: Methods to plot chronograms

Plot a Chronogram and Add Age Data to Nodes

Description

'plot_node_ages' plots a chronograms given in 'phy' and adds age data [points()] given in 'calibration_summary' to the corresponding nodes.

Usage

plot_node_ages(
  phy,
  time_depth = NULL,
  plot_type = "phyloch",
  mai1,
  mai2,
  mai3,
  mai4,
  omi1,
  omi2,
  omi3,
  omi4,
  title = "Chronogram",
  cex_title = graphics::par("cex"),
  pos_title = 1,
  cex_tiplabels = graphics::par("cex"),
  geologic_timescale = "strat2012",
  geologic_unit = "period",
  pos_axis = 1,
  cex_axis = graphics::par("cex"),
  axis_label = "Time (MYA)",
  center_axislabel = 0.5,
  cex_axislabel = graphics::par("cex"),
  calibration_summary,
  pch = 20,
  color_pch,
  transparent_pch = NULL,
  cex_pch = graphics::par("cex"),
  color_bars = "#80808050",
  lty_bars = "solid",
  lwd_bars = 7,
  add_legend = TRUE,
  cex_legend = cex_axislabel * 0.5,
  x_legend = NULL,
  y_legend = NULL,
  ...
)

Arguments

phy	A 'phylo' object with branch length proportional to time.
time_depth	A numeric vector indicating the upper limit for the time scale on the x axis.
plot_type	A character vector of length one indicating the type of plot to generate. Options are: "ape" It uses the functions [ape::plot.phylo()] and [ape::axisPhylo()]. "phyloch" It uses the functions [ape::plot.phylo()] and [phyloch::axisGeo()]. "strap" It uses the function [strap::geoscalePhylo()] from the package [strap]. "phytools" Not implemented yet. It will use functions from the package [phytools]
mai1	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.
mai2	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.
mai3	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.
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.
omi1	A numeric value indicating outter plot margin sizes in inches.
omi2	A numeric value indicating outter plot margin sizes in inches.
omi3	A numeric value indicating outter plot margin sizes in inches.
omi4	A numeric value indicating outter plot margin sizes in inches.
title	A character string providing the title for the plot.
cex_title	A numeric indicating character expansion for the title. Default to value given by 'graphics::par("cex")'.
pos_title	Indicates the line position of the title. Default to 1.
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")'.
geologic_timescale	A dataframe of geochronological limits.
geologic_unit	A character vector used to select geological time units that shall be displayed. When using gradstein04, "eon", "era", "period", "epoch", and "stage" are available.
pos_axis	Indicates the line position of the axis. Default to 1.
cex_axis	A numeric indicating character expansion for the axis. Default to value given by 'graphics::par("cex")'.
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.
center_axislabel	A numeric indicating centering position of time axis label. Default to 0.5.
cex_axislabel	A numeric indicating character expansion for the time axis label. Default to value given by 'graphics::par("cex")'.
calibration_summary	An output of [datelife:::summary.matchedCalibrations()]
pch	A numeric vector indicating the symbol to plot age points. See [graphics::par()] for options. Defaults to 20 = "bullet circle".
color_pch	A named vector of colors. Names must correspond to study names in 'calibration_summary$in_phy$references'. If vector is not named, colors will be recycled.
transparent_pch	A numeric value ranging from 10-99, indicating transparency for 'color_pch'. Default to 'NULL', no transparency.
cex_pch	A numeric value indicating **c**haracter **ex**pansion (i.e., size scaling factor) of node age point symbols defined by 'pch'. Default to 1.
color_bars	A character vector of one element indicating the color for node age distribution bars. Defaults to "#80808050", which is hex for gray ("#808080") with 50% transparency.
lty_bars	A numeric vector or character string indicating the plotting line type for bars. See [graphics::par()] for options. Default to "solid".
lwd_bars	A numeric vector indicating the line width for age distribution bars. See [graphics::par()] for options. Default to 7.
add_legend	Default to 'TRUE', adds a legend to the left of the plot.
cex_legend	A numeric value indicating **c**haracter **ex**pansion (i.e., size scaling factor) of legend. Default to one half the size of the axis label, 'cex_axislabel * 0.5'.
x_legend	the x co-ordinate to be used to position the legend on the left side of the plot.
y_legend	the y co-ordinate to be used to position the legend on the left side of the plot.
...	Arguments passed on to ape::plot.phylo x an object of class "phylo" or of class "multiPhylo". type a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial", "tidy", or any unambiguous abbreviation of these. use.edge.length a logical indicating whether to use the edge lengths of the phylogeny to draw the branches (the default) or not (if FALSE). This option has no effect if the object of class "phylo" has no ‘edge.length’ element. node.pos a numeric taking the value 1 or 2 which specifies the vertical position of the nodes with respect to their descendants. If NULL (the default), then the value is determined in relation to ‘type’ and ‘use.edge.length’ (see details). show.tip.label a logical indicating whether to show the tip labels on the phylogeny (defaults to TRUE, i.e. the labels are shown). show.node.label a logical indicating whether to show the node labels on the phylogeny (defaults to FALSE, i.e. the labels are not shown). edge.color a vector of mode character giving the colours used to draw the branches of the plotted phylogeny. These are taken to be in the same order than the component edge of phy. If fewer colours are given than the length of edge, then the colours are recycled. edge.width a numeric vector giving the width of the branches of the plotted phylogeny. These are taken to be in the same order than the component edge of phy. If fewer widths are given than the length of edge, then these are recycled. edge.lty same as the previous argument but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash. node.color a vector of mode character giving the colours used to draw the perpendicular lines associated with each node of the plotted phylogeny. These are taken to be in the same order than the component node of phy. If fewer colours are given than the length of node, then the colours are recycled. node.width as the previous argument, but for line widths. node.lty as the previous argument, but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash. font an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic). cex a numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters. adj a numeric specifying the justification of the text strings of the labels: 0 (left-justification), 0.5 (centering), or 1 (right-justification). This option has no effect if type = "unrooted". If NULL (the default) the value is set with respect of direction (see details). srt a numeric giving how much the labels are rotated in degrees (negative values are allowed resulting in clock-like rotation); the value has an effect respectively to the value of direction (see Examples). This option has no effect if type = "unrooted". no.margin a logical. If TRUE, the margins are set to zero and the plot uses all the space of the device (note that this was the behaviour of plot.phylo up to version 0.2-1 of ‘ape’ with no way to modify it by the user, at least easily). root.edge a logical indicating whether to draw the root edge (defaults to FALSE); this has no effect if ‘use.edge.length = FALSE’ or if ‘type = "unrooted"’. label.offset a numeric giving the space between the nodes and the tips of the phylogeny and their corresponding labels. This option has no effect if type = "unrooted". underscore a logical specifying whether the underscores in tip labels should be written as spaces (the default) or left as are (if TRUE). x.lim a numeric vector of length one or two giving the limit(s) of the x-axis. If NULL, this is computed with respect to various parameters such as the string lengths of the labels and the branch lengths. If a single value is given, this is taken as the upper limit. y.lim same than above for the y-axis. direction a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards". lab4ut (= labels for unrooted trees) a character string specifying the display of tip labels for unrooted trees (can be abbreviated): either "horizontal" where all labels are horizontal (the default if type = "u"), or "axial" where the labels are displayed in the axis of the corresponding terminal branches. This option has an effect if type = "u", "f", or "r". tip.color the colours used for the tip labels, eventually recycled (see examples). plot a logical controlling whether to draw the tree. If FALSE, the graphical device is set as if the tree was plotted, and the coordinates are saved as well. rotate.tree for "fan", "unrooted", or "radial" trees: the rotation of the whole tree in degrees (negative values are accepted). open.angle if type = "f" or "r", the angle in degrees left blank. Use a non-zero value if you want to call axisPhylo after the tree is plotted. node.depth an integer value (1 or 2) used if branch lengths are not used to plot the tree; 1: the node depths are proportional to the number of tips descending from each node (the default and was the only possibility previously), 2: they are evenly spaced. align.tip.label a logical value or an integer. If TRUE, the tips are aligned and dotted lines are drawn between the tips of the tree and the labels. If an integer, the tips are aligned and this gives the type of the lines (lty).

Details

Plot are margin sizes as defined by [graphics::par()$mai] and [graphics::par()$omi] are overruled within the function. To modify them you have to use the arguments 'mai1', 'mai2', 'mai3' and 'mai4', and omi1, omi2, omi3 and omi4.

phylotastic/datelifeplot documentation built on July 14, 2022, 12:35 p.m.