plotAncStatesPie: plot Ancestral States Pie

In RevGadgets: Visualization and Post-Processing of 'RevBayes' Analyses

plot Ancestral States Pie

Description

Plot character states and posterior probabilities as pies on nodes.

Usage

plotAncStatesPie(
  t,
  cladogenetic = FALSE,
  tip_labels = TRUE,
  tip_labels_size = 2,
  tip_labels_offset = 1,
  tip_labels_italics = FALSE,
  tip_labels_formatted = FALSE,
  tip_labels_remove_underscore = TRUE,
  tip_labels_states = FALSE,
  tip_labels_states_size = 2,
  tip_labels_states_offset = 0.1,
  node_labels_as = NULL,
  node_labels_size = 2,
  node_labels_offset = 0.1,
  pie_colors = "default",
  node_pie_size = 1,
  shoulder_pie_size = node_pie_size,
  tip_pies = TRUE,
  tip_pie_size = 0.5,
  node_pie_nudge_x = 0,
  node_pie_nudge_y = 0,
  tip_pie_nudge_x = node_pie_nudge_x,
  tip_pie_nudge_y = node_pie_nudge_y,
  shoulder_pie_nudge_x = node_pie_nudge_x,
  shoulder_pie_nudge_y = node_pie_nudge_y,
  state_transparency = 0.75,
  timeline = FALSE,
  geo = timeline,
  geo_units = list("epochs", "periods"),
  time_bars = timeline,
  ...
)

Arguments

t	(treedata object; none) Output of processAncStates() function containing tree and ancestral states.
cladogenetic	(logical; FALSE) Plot shoulder pies of cladogenetic analyses?
tip_labels	(logical; TRUE) Label taxa labels at tips?
tip_labels_size	(numeric; 2) Size of tip labels.
tip_labels_offset	(numeric; 1) Horizontal offset of tip labels from tree.
tip_labels_italics	(logical; FALSE) Italicize tip labels?
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 from tip labels?
tip_labels_states	(logical; FALSE) Optional plotting of text at tips in addition to taxa labels. Will plot the MAP state label.
tip_labels_states_size	(numeric; 2) Size of state labels at tips. Ignored if tip_labels_states is FALSE.
tip_labels_states_offset	(numeric; 0.1) Horizontal offset of tip state labels. Ignored if tip_labels_states = NULL.
node_labels_as	(character; NULL) Optional plotting of text at nodes. Possible values are "state" for the MAP ancestral states, "node_posterior" for the posterior probability of the node on the tree, “state_posterior” for the posterior probability of the MAP, or NULL for not plotting any text at the nodes (default).
node_labels_size	(numeric; 2) Size of node labels text. Ignored if node_labels_as = NULL.
node_labels_offset	(numeric; 0.1) Horizontal offset of node labels from nodes. Ignored if node_labels_as = NULL.
pie_colors	("character"; "default") Colors for states in pies. If "default", plots the default RevGadgets colors. Provide a character vector of hex codes or other R-readable colors the same length of the number of character states. Names of the vector should correspond to state labels.
node_pie_size	(numeric; 1) Size (diameter) of the pies at nodes.
shoulder_pie_size	(numeric; node_pie_size) Size (diameter) of the pies at shoulders for cladogenetic plots.
tip_pies	(logical; TRUE) Plot pies tips?
tip_pie_size	(numeric; 0.5) Size (diameter) of the pies at tips.
node_pie_nudge_x	(numeric; 0) If pies aren't centered, adjust by nudging
node_pie_nudge_y	(numeric; 0) If pies aren't centered, adjust by nudging
tip_pie_nudge_x	(numeric; node_pie_nudge_x) If pies aren't centered, adjust by nudging
tip_pie_nudge_y	(numeric; node_pie_nudge_y) If pies aren't centered, adjust by nudging
shoulder_pie_nudge_x	(numeric; node_pie_nudge_x) If pies aren't centered, adjust by nudging
shoulder_pie_nudge_y	(numeric; node_pie_nudge_y) If pies aren't centered, adjust by nudging
state_transparency	(integer; 0.75) Alpha (transparency) of state symbols- varies from 0 to 1.
timeline	(logical; FALSE) Plot tree with labeled x-axis with timescale in MYA.
geo	(logical; timeline) Add a geological timeline? Defaults to the same as timeline.
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.
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.
...	(various) Additional arguments passed to ggtree::ggtree().

Value

A ggplot object

Examples

# Standard ancestral state reconstruction example

# process file and assign state labels
file <- system.file("extdata",
                    "comp_method_disc/ase_freeK.tree",
                    package="RevGadgets")
example <- processAncStates(file,
                            state_labels = c("1" = "Awesome",
                                             "2" = "Beautiful",
                                             "3" = "Cool!"))
# plot (this may take a while)
plotAncStatesPie(t = example)

# DEC Biogeographic range evolution example (with timeline)

# process file
file <- system.file("extdata", "dec/simple.ase.tre", package="RevGadgets")

# labels that correspond to each region/ possible combination of regions
labs <- c("1" = "K", "2" = "O", "3" = "M", "4" = "H", "5" = "KO",
          "6" = "KM", "7" = "OM", "8" = "KH", "9" = "OH", "10" = "MH",
          "11" = "KOM", "12" = "KOH", "13" = "KMH", "14" = "OMH",
          "15" = "KOMH")
dec_example  <- processAncStates(file , state_labels = labs)
# Use the state_labels in returned tidytree object to define color palette
# These state_labels may be a subset of the labels you provided
# (not all possible regions may be sampled in the dataset)
colors <- colorRampPalette(colFun(12))(length(dec_example@state_labels))
names(colors) <- dec_example@state_labels

# plot
plotAncStatesPie(t = dec_example, pie_colors = colors, tip_labels_size = 3,
        cladogenetic = TRUE, tip_labels_offset = 0.25, timeline = TRUE,
        geo = FALSE) +
        ggplot2::theme(legend.position = c(0.1, 0.75))

RevGadgets documentation built on May 29, 2024, 10:03 a.m.