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Add PhyloPics to a phylogenetic tree plotted with base R

Source: R/add_phylopic_tree.R
add_phylopic_tree.Rd

Specify existing images, taxonomic names, or PhyloPic uuids to add PhyloPic silhouettes alongside the associated leaves of a phylogenetic tree that has been plotted in the active graphics device using the base R graphics functions.

Usage

add_phylopic_tree(
  tree,
  tip = names(img) %||% names(uuid) %||% names(name) %||% name,
  img = NULL,
  name = if (is.null(img) && is.null(uuid)) tip else NULL,
  uuid = NULL,
  width,
  padding = NULL,
  relWidth = 0.06,
  relPadding = 1/200,
  hjust = 0,
  ...
)

Arguments

tree

The phylogenetic tree object of class phylo on which to add the silhouette.

tip

The tip labels against which to add the silhouettes. If not specified, the names of the img, uuid or name vector are used.

img

A Picture or png array object, e.g., from using get_phylopic().

name

character. A taxonomic name to be passed to get_uuid().

uuid

character. A valid uuid for a PhyloPic silhouette (such as that returned by get_uuid() or pick_phylopic()).

width

numeric. Width of the silhouette in coordinate space. If "NULL", the default, and height is also "NULL", the silhouette will be as large as fits in the plot area. If "NULL" and height is specified, the width is determined by the aspect ratio of the original image. One or both of height and width must be "NULL".

padding, relPadding

Distance to inset each silhouette from the right edge of the plotting area, in the plot coordinate system (padding) or relative to the size of the plotting area (relPadding). Negative values offset to the right.

relWidth

The width of each silhouette relative to the plotting area.

hjust

numeric. A numeric vector between 0 and 1 specifying horizontal justification (left = 0, center = 0.5, right = 1).

...

Further arguments to pass to add_phylopic_base().

See also

For trees plotted using ggtree, see geom_phylopic().

Author

Martin R. Smith (martin.smith@durham.ac.uk)

Examples

if (FALSE) { # \dontrun{
 # Load the ape library to work with phylogenetic trees
library("ape")

# Read a phylogenetic tree
tree <- ape::read.tree(text = "(cat, (dog, mouse));")

# Set a large right margin to accommodate the silhouettes
par(mar = c(1, 1, 1, 10))

# Plot the tree
plot(tree)

# Add a PhyloPic silhouette of a cat to the tree
add_phylopic_tree(
  tree, # Must be the tree that was plotted
  "cat", # Which leaf should the silhouette be plotted against?
  uuid = "23cd6aa4-9587-4a2e-8e26-de42885004c9", # Silhouette to plot
  relWidth = 0.2,
  fill = "brown"
)
} # }