treePlotter: Rboretum Tree Plot Generator
In BobLiterman/Rboretum: Compare Phylogenetic Trees and Alignment Support Values

treePlotter

R Documentation

Rboretum Tree Plot Generator

Description

Given a phylo or multiPhylo object (tree), and some optional metadata, this ggtree wrapper returns a ggtree plot object, adjusted with possible arguments

Usage

treePlotter(
  tree,
  basic_plot,
  tree_support,
  plot_root_support,
  clade_support,
  geom_size,
  log_transform,
  scale_range,
  use_pies,
  pie_colors,
  pie_xnudge,
  pie_ynudge,
  pie_legend_position,
  branch_length,
  branch_weight,
  node_label,
  node_label_font_size,
  node_label_fontface,
  node_label_color,
  node_label_box,
  node_label_nudge,
  taxa_font_size,
  taxa_fontface,
  taxa_offset,
  xmax,
  xmin,
  reverse_x,
  to_color,
  colors,
  highlight_legend,
  color_branches,
  plot_title,
  plot_title_size,
  plot_title_fontface,
  legend_shape_size,
  legend_font_size,
  legend_title_size,
  geom_alpha,
  geom_color
)

Arguments

`tree`	Tree(s) to plot. Options include: A single, rooted phylo object; or, A rooted multiPhylo object where all trees share 3+ taxa [Only unique topologies plotted, from most to least common]
`basic_plot`	OPTIONAL: If providing a multiPhylo and TRUE, plot all trees as stored and disable support functions [Default: FALSE, plot unique topologies after pruning to common taxa]
`tree_support`	OPTIONAL: Output of getAlignmentSupport, including data from all clades in 'tree'
`plot_root_support`	OPTIONAL: If TRUE and plotting node support via 'tree_support', include root nodes [Default: FALSE, do not include support for root nodes]
`clade_support`	OPTIONAL: Output of getTreeClades(return_counts=TRUE), including data from all clades in 'tree'
`geom_size`	OPTIONAL: If plotting support via tree_support, how should geom_nodepoint (or pies) be sized? Options include: Single numeric value: All geom_nodepoint geoms will be this size [Default: 4] c(min,max): If used with tree_support, geoms will be sized based on the total support across datasets and rescaled between min and max.
`log_transform`	OPTIONAL: If TRUE and plotting tree_support, log transform values prior to rescaling [Default: FALSE]
`scale_range`	OPTIONAL: If plotting tree_support, supply a min and max of values to be scaled. Values outside this range will be displayed as the otherwise min/max geom size. [Default: scale all data]
`use_pies`	OPTIONAL: If TRUE and tree_support contains inforomation from 2+ datasets, data from tree_support will be displayed as an inset pie chart rather than a geom_nodepoint [Default: FALSE, use geom_nodepoint; DEACTIVATED WHEN clade_support IS PROVIDED]
`pie_colors`	OPTIONAL If plotting with pies, a vector of colors with one item per support column [Default: ggplot default colors]
`pie_xnudge`	OPTIONAL: Set ggtree pie label hjust [Default: 0]
`pie_ynudge`	OPTIONAL: Set ggtree pie label yjust [Default: 0]
`pie_legend_position`	OPTIONAL: Numerical vector of length four specifying legend xmin,xmax,ymin,ymax respectively. [Default = c(1,1,1,1); Necessary oddity of generating a legend for nodepie data]
`branch_length`	OPTIONAL: TRUE [plot tree(s) with branch lengths]; FALSE [Default: plot cladogram(s)]
`branch_weight`	OPTIONAL: Set ggtree branch thickness [Default: 1]
`node_label`	OPTIONAL: Choice of node labels include: "bs": Bootstrap value [Default] "none": No node labels "node": Node number "support": Raw total support count (Only with tree_support) "clade": Percent of trees in clade_support that support this clade (Only with clade_support)
`node_label_font_size`	OPTIONAL: Set ggtree node label font size [Default: 5]
`node_label_fontface`	OPTIONAL: Set node label fontface. Options include: "plain" [Default] "bold" "italic" "bold.italic"
`node_label_color`	OPTIONAL: Set ggtree node label color [Default: 'black']
`node_label_box`	OPTIONAL: Set ggtree node label as a label with a white background [Default: TRUE]
`node_label_nudge`	OPTIONAL: Set ggtree node label nudge_x [Default: 0]
`taxa_font_size`	OPTIONAL: Set ggtree tip label font size [Default: 5]
`taxa_fontface`	OPTIONAL: Set tip label fontface. Options include: "plain" [Default] "bold" "italic" "bold.italic"
`taxa_offset`	OPTIONAL: Set ggtree tip label offset [Default: 0]
`xmax`	OPTIONAL: Set ggplot xlim upper limit (e.g if long tip labels run off plot)
`xmin`	OPTIONAL: Set ggplot xlim lower limit (Must be used along with xmax [Default: 0])
`reverse_x`	OPTIONAL: TRUE [plot tree with tips on left]; FALSE [Default: plot tree with tips on right]
`to_color`	OPTIONAL: Color tips or clades via: Character vector of taxa, all to be colored the same color List of groups of taxa, each of which will have their own color. List can be named for use with a legend (set highlight_legend == TRUE)
`colors`	OPTIONAL: Colors for clade highlighting. Must be hex or valid R colors. Provide a color for each group (1 if character vector, 1 for each group if named list) or default colors will be used.
`highlight_legend`	OPTIONAL: Include a legend for colored tips, given a list (disabled if providing clade_support); [Default: False: No highlight legend]
`color_branches`	OPTIONAL: If TRUE and coloring taxa or clades, color the branches rather than the tip labels [Default: FALSE, colorize tip labels; DEACTIVATED IF clade_support is provided]
`plot_title`	OPTIONAL: Character vector containing plot titles (1 per tree) [Default: No title for phylo, tree name for multiPhylo]
`plot_title_size`	OPTIONAL: Set ggplot title font size [Default: 14]
`plot_title_fontface`	OPTIONAL: Set ggplot title fontface "plain" "bold" [Default] "italic" "bold.italic"
`legend_shape_size`	OPTIONAL: ggplot2 size for legend icons [Default: 5]
`legend_font_size`	OPTIONAL: ggplot2 size for legend font [Default: 10]
`legend_title_size`	OPTIONAL: ggplot size for legend title [Default: 10]
`geom_alpha`	OPTIONAL: ggplot2 alpha value for geom_nodepoint (or pies) [Default: 0.9]
`geom_color`	OPTIONAL: ggplot2 color value for geom_nodepoint if clade_support not provided [Default: 'red']