plotTree: Plot tree

Description

Plots a single tree, such as an MCC or MAP tree.

Usage

plotTree(
  tree,
  timeline = FALSE,
  geo_units = list("epochs", "periods"),
  geo = timeline,
  time_bars = timeline,
  node_age_bars = FALSE,
  age_bars_color = "blue",
  age_bars_colored_by = NULL,
  age_bars_width = 1.5,
  node_labels = NULL,
  node_labels_color = "black",
  node_labels_size = 3,
  node_labels_offset = 0,
  tip_labels = TRUE,
  tip_labels_italics = FALSE,
  tip_labels_formatted = FALSE,
  tip_labels_remove_underscore = TRUE,
  tip_labels_color = "black",
  tip_labels_size = 3,
  tip_labels_offset = 0,
  node_pp = FALSE,
  node_pp_shape = 16,
  node_pp_color = "black",
  node_pp_size = "variable",
  branch_color = "black",
  color_branch_by = NULL,
  line_width = 1,
  tree_layout = "rectangular",
  ...
)

Value

returns a single plot object.

Arguments

tree: (list of lists of treedata objects; no default) Name of a list of lists of treedata objects, such as produced by readTrees(). This object should only contain only one summary tree from one trace file. If it contains multiple trees or multiple traces, only the first will be used.
timeline: (logical; FALSE) Plot time tree with labeled x-axis with timescale in MYA.
geo_units: (list; list("epochs", "periods")) Which geological units to include in the geo timescale. May be "periods", "epochs", "stages", "eons", "eras", or a list of two of those units.
geo: (logical; timeline) Add a geological timeline? Defaults to the same as timeline.
time_bars: (logical; timeline) Add vertical gray bars to indicate geological timeline units if geo == TRUE or regular time intervals (in MYA) if geo == FALSE.
node_age_bars: (logical; FALSE) Plot time tree with node age bars?
age_bars_color: (character; "blue") Color for node age bars. If age_bars_colored_by specifies a variable (not NULL), you must provide two colors, low and high values for a gradient. Colors must be either R valid color names or valid hex codes.
age_bars_colored_by: (character; NULL) Specify column to color node age bars by, such as "posterior". If null, all node age bars plotted the same color, specified by age_bars_color
age_bars_width: (numeric; 1.5) Change line width for age bars
node_labels: (character; NULL) Plot text labels at nodes, specified by the name of the corresponding column in the tidytree object. If NULL, no text is plotted.
node_labels_color: (character; "black") Color to plot node_labels, either as a valid R color name or a valid hex code.
node_labels_size: (numeric; 3) Size of node labels
node_labels_offset: (numeric; 0) Horizontal offset of node labels from nodes.
tip_labels: (logical; TRUE) Plot tip labels?
tip_labels_italics: (logical; FALSE) Plot tip labels in italics?
tip_labels_formatted: (logical; FALSE) Do the tip labels contain manually added formatting information? Will set parse = TRUE in geom_text() and associated functions to interpret formatting. See ?plotmath for more. Cannot be TRUE if tip_labels_italics = TRUE.
tip_labels_remove_underscore: (logical; TRUE) Remove underscores in tip labels?
tip_labels_color: (character; "black") Color to plot tip labels, either as a valid R color name or a valid hex code.
tip_labels_size: (numeric; 3) Size of tip labels
tip_labels_offset: (numeric; 1) Horizontal offset of tip labels from tree.
node_pp: (logical; FALSE) Plot posterior probabilities as symbols at nodes? Specify symbol aesthetics with node_pp_shape, node_pp_color, and node_pp_size.
node_pp_shape: (integer; 1) Integer corresponding to point shape (value between 0-25). See ggplot2 documentation for details: https://ggplot2.tidyverse.org/articles/ggplot2-specs.html#point
node_pp_color: (character; "black") Color for node_pp symbols, either as valid R color name(s) or hex code(s). Can be a single character string specifying a single color, or a vector of length two specifying two colors to form a gradient. In this case, posterior probabilities will be indicated by color along the specified gradient.
node_pp_size: (numeric or character; 1) Size for node_pp symbols. If numeric, the size will be fixed at the specified value. If a character, it should specify "variable", indicating that size should be scaled by the posterior value. Size regulates the area of the shape, following ggplot2 best practices: https://ggplot2.tidyverse.org/reference/scale_size.html)
branch_color: (character; "black") A single character string specifying the color (R color name or hex code) for all branches OR a vector of length 2 specifying two colors for a gradient, used to color the branches according to the variable specified in color_branch_by. If only 1 color is provided and you specify color_branch_by, default colors will be chosen (low = "#005ac8", high = "#fa7850").
color_branch_by: (character; NULL ) Optional name of one quantitative variable in the treedata object to color branches, such as a rate.
line_width: (numeric; 1) Change line width for branches
tree_layout: (character; "rectangular") Tree shape layout, passed to ggtree(). Options are 'rectangular', 'cladogram', 'slanted', 'ellipse', 'roundrect', 'fan', 'circular', 'inward_circular', 'radial', 'equal_angle', 'daylight', or 'ape'.
...: (various) Additional arguments passed to ggtree::ggtree().

Details

Plots a single tree, such as an MCC or MAP tree, with optionally labeled posterior probabilities at nodes, a timescale plotted on the x - axis, and 95% CI for node ages.

Examples

Run this code

# \donttest{
# Example of standard tree plot

file <- system.file("extdata",
                    "sub_models/primates_cytb_GTR_MAP.tre",
                    package="RevGadgets")
tree <- readTrees(paths = file)
# Reroot tree before plotting
tree_rooted <- rerootPhylo(tree = tree, outgroup = "Galeopterus_variegatus")
# Plot
p <- plotTree(tree = tree_rooted, node_labels = "posterior");p

# Plot unladderized tree
p <- plotTree(tree = tree_rooted,
              node_labels = "posterior",
              ladderize = FALSE);p

# We can add a scale bar:
p + ggtree::geom_treescale(x = -0.35, y = -1)

# Example of coloring branches by rate
file <- system.file("extdata",
                    "relaxed_ou/relaxed_OU_MAP.tre",
                    package="RevGadgets")
tree <- readTrees(paths = file)
p <- plotTree(tree = tree,
              node_age_bars = FALSE,
              node_pp = FALSE,
              tip_labels_remove_underscore = TRUE,
              tip_labels_italics = FALSE,
              color_branch_by = "branch_thetas",
              line_width = 1.7) +
       ggplot2::theme(legend.position=c(.1, .9));p
# }

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