add_phylopic: Annotate a ggplot plot with PhyloPics

In sckott/rphylopic: Get Silhouettes of Organisms from PhyloPic

Annotate a ggplot plot with PhyloPics

Description

Specify existing images, taxonomic names, or PhyloPic uuids to add PhyloPic silhouettes as a separate layer to an existing ggplot plot.

Usage

add_phylopic(
  img = NULL,
  name = NULL,
  uuid = NULL,
  filter = NULL,
  x,
  y,
  ysize = deprecated(),
  height = NA,
  width = NA,
  alpha = 1,
  color = NA,
  fill = "black",
  horizontal = FALSE,
  vertical = FALSE,
  angle = 0,
  hjust = 0.5,
  vjust = 0.5,
  remove_background = TRUE,
  verbose = FALSE
)

Arguments

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()).
filter	character. Filter by usage license if name is defined. 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.
x	numeric. x value of the silhouette center.
y	numeric. y value of the silhouette center.
ysize	use the height or width argument instead.
height	numeric. Height of the silhouette in coordinate space. If "NA", the default, and width is "NA", the silhouette will be as large as fits in the plot area. If "NA" and width is specified, the height is determined by the aspect ratio of the original image. One or both of height and width must be "NA".
width	numeric. Width of the silhouette in coordinate space. If "NA", the default, and height is "NA", the silhouette will be as large as fits in the plot area. If "NA", the default, 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 "NA".
alpha	numeric. A value between 0 and 1, specifying the opacity of the silhouette (0 is fully transparent, 1 is fully opaque).
color	character. Color of silhouette outline. If "original" or NA is specified, the original color of the silhouette outline will be used (usually the same as "transparent"). To remove the outline, you can set this to "transparent".
fill	character. Color of silhouette. If "original" is specified, the original color of the silhouette will be used (usually the same as "black"). If color is specified and fill is NA, color will be used as the fill color (for backwards compatibility). To remove the fill, you can set this to "transparent".
horizontal	logical. Should the silhouette be flipped horizontally?
vertical	logical. Should the silhouette be flipped vertically?
angle	numeric. The number of degrees to rotate the silhouette clockwise. The default is no rotation.
hjust	numeric. A numeric vector between 0 and 1 specifying horizontal justification (left = 0, center = 0.5, right = 1). Note that, due to the enforcement of the silhouette's aspect ratio, there may be unexpected behavior due to interactions between the aspect ratio of the plot and the aspect ratio of the silhouette.
vjust	numeric. A numeric vector between 0 and 1 specifying vertical justification (top = 1, middle = 0.5, bottom = 0). Note that, due to the enforcement of the silhouette's aspect ratio, there may be unexpected behavior due to interactions between the aspect ratio of the plot and the aspect ratio of the silhouette.
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())?

Details

One (and only one) of img, name, or uuid must be specified. Use parameters x, y, and ysize to place the silhouette at a specified position on the plot. The aspect ratio of the silhouette will always be maintained.

x and/or y may be vectors of numeric values if multiple silhouettes should be plotted at once. In this case, any other arguments (except for remove_background) may also be vectors of values, which will be recycled as necessary.

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.

Examples

## Not run: 
# Put a silhouette behind a plot based on a taxonomic name
library(ggplot2)
ggplot(iris) +
  add_phylopic(x = 6.1, y = 3.2, name = "Iris", alpha = 0.2) +
  geom_point(aes(x = Sepal.Length, y = Sepal.Width))

# Put a silhouette in several places based on UUID
posx <- runif(10, 0, 10)
posy <- runif(10, 0, 10)
heights <- runif(10, 0.4, 2)
angle <- runif(10, 0, 360)
hor <- sample(c(TRUE, FALSE), 10, TRUE)
ver <- sample(c(TRUE, FALSE), 10, TRUE)
fills <- sample(c("black", "darkorange", "grey42", "white"), 10,
  replace = TRUE)
alpha <- runif(10, 0.3, 1)

p <- ggplot(data.frame(cat.x = posx, cat.y = posy), aes(cat.x, cat.y)) +
  geom_blank() +
  add_phylopic(uuid = "23cd6aa4-9587-4a2e-8e26-de42885004c9",
               x = posx, y = posy, height = heights,
               fill = fills, alpha = alpha, angle = angle,
               horizontal = hor, vertical = ver)
p + ggtitle("R Cat Herd!!")

## End(Not run)

sckott/rphylopic documentation built on Oct. 13, 2024, 12:27 p.m.