geom_phylopic: Geom for adding PhyloPic silhouettes to a plot

In rphylopic: Get Silhouettes of Organisms from PhyloPic

Geom for adding PhyloPic silhouettes to a plot

Description

This geom acts like ggplot2::geom_point(), except that the specified silhouettes are used as points. Silhouettes can be specified by their name, uuid, or image objects (img).

Usage

geom_phylopic(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  na.rm = FALSE,
  show.legend = FALSE,
  inherit.aes = TRUE,
  remove_background = TRUE,
  verbose = FALSE,
  filter = NULL
)

Arguments

mapping	Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.
data	The data to be displayed in this layer. There are three options: If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot(). A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created. A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).
stat	The statistical transformation to use on the data for this layer, either as a ggproto Geom subclass or as a string naming the stat stripped of the stat_ prefix (e.g. "count" rather than "stat_count")
position	Position adjustment, either as a string naming the adjustment (e.g. "jitter" to use position_jitter), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
...	Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.
na.rm	If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.
show.legend	logical. Should this layer be included in the legends? FALSE, the default, never includes, NA includes if any aesthetics are mapped, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.
inherit.aes	If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().
remove_background	logical. Should any white background be removed from the silhouette(s)? See recolor_phylopic() for details.
verbose	logical. Should the attribution information for the used silhouette(s) be printed to the console (see get_attribution())?
filter	character. Filter by usage license if using the name aesthetic. Use "by" to limit results to images which do not require attribution, "nc" for images which allows commercial usage, and "sa" for images without a ShareAlike clause. The user can also combine these filters as a vector.

Details

One (and only one) of the img, name, or uuid aesthetics must be specified. The img aesthetic can be Picture objects or png array objects, e.g., from using get_phylopic(). Use the x and y aesthetics to place the silhouettes at specified positions on the plot. The size aesthetic specifies the height of the silhouettes in the units of the y axis. The aspect ratio of the silhouettes will always be maintained.

The color (default: "black"), fill (default: NA), and alpha (default:

1. aesthetics can be used to change the outline color, fill color, and transparency (outline and fill) of the silhouettes, respectively. If color is specified and fill is NA the outline and fill color will be the same. If "original" is specified for the color aesthetic, the original color of the silhouette outline will be used (usually the same as "transparent"). If "original" is specified for the fill aesthetic, the original color of the silhouette body will be used (usually the same as "black").

The horizontal and vertical aesthetics can be used to flip the silhouettes. The angle aesthetic can be used to rotate the silhouettes. When specifying a horizontal and/or vertical flip and a rotation, the flip(s) will always occur first. If you would like to customize this behavior, you can flip and/or rotate the image within your own workflow using flip_phylopic() and rotate_phylopic().

Note that png array objects can only be rotated by multiples of 90 degrees. Also, outline colors do not currently work for png array objects.

Aesthetics

geom_phylopic understands the following aesthetics:

• x (required)

• y (required)

• img/uuid/name (one, and only one, required)

• size

• color/colour

• fill

• alpha

• horizontal

• vertical

• angle

  Learn more about setting these aesthetics in add_phylopic().

Examples

## Not run: 
library(ggplot2)
df <- data.frame(x = c(2, 4), y = c(10, 20),
                 name = c("Felis silvestris catus", "Odobenus rosmarus"))
ggplot(df) +
  geom_phylopic(aes(x = x, y = y, name = name),
                color = "purple", size = 10) +
  facet_wrap(~name) +
  coord_cartesian(xlim = c(1,6), ylim = c(5, 30))

## End(Not run)

rphylopic documentation built on Nov. 2, 2023, 6:13 p.m.