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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. The current functionality assumes that the tree is not in a circular configuration and has a "rightwards" direction.

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,
  align = "tip",
  width,
  padding = NULL,
  relWidth = 0.06,
  relPadding = if (align == "tip") 1/200 else -1/200,
  hjust = if (align == "tip") 0 else 1,
  ...
)

Arguments

tree

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

tip

character. 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()).

align

character. Should each silhouette be aligned to its respective tip ("tip", the default) or to the right-hand side of the plotting area ("plot")? If "tip" is specified, the silhouette is placed at the x coordinate of the respective tip, plus any horizontal padding specified by padding or relPadding. If "plot" is specified, the silhouette is placed at the right-hand side of the plotting area, determined by par("usr"), plus any horizontal padding specified by padding or relPadding.

width, relWidth

numeric. The width of each silhouette, in the plot coordinate system (width) or relative to the size of the plotting area (relWidth). If "NULL" and height is specified, the width is determined by the aspect ratio of the original image. One of height and width must be "NULL".

padding, relPadding

numeric. Horizontal padding for each silhouette from its respective x value, in the plot coordinate system (padding) or relative to the size of the plotting area (relPadding). Negative values offset to the left.

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"
)
} # }