add_phylopic_base {rphylopic}

Add PhyloPics to a base R plot

Description

Specify existing images, taxonomic names, or PhyloPic uuids to add PhyloPic silhouettes on top of an existing base R plot (like points()).

Usage

add_phylopic_base(
  img = NULL,
  name = NULL,
  uuid = NULL,
  filter = NULL,
  x = NULL,
  y = NULL,
  ysize = NULL,
  alpha = 1,
  color = NA,
  fill = "black",
  horizontal = FALSE,
  vertical = FALSE,
  angle = 0,
  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. Ignored if y and ysize are not specified.

y

numeric. y value of the silhouette center. Ignored if x and ysize are not specified.

ysize

numeric. Height of the silhouette. The width is determined by the aspect ratio of the original image. Ignored if x and y are not specified.

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.

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. If all three of these parameters are unspecified, then the silhouette will be plotted to the full height and width of the plot. The aspect ratio of the silhouette will always be maintained (even when a plot is resized). However, if the plot is resized after plotting the silhouette, the absolute size and/or position of the silhouette may change.

Any argument (except for remove_background) may be a vector of values if multiple silhouettes should be plotted. In this case, all other arguments may also be vectors of values, which will be recycled as necessary to the length of the longest vector argument.

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: 
# single image
plot(1, 1, type = "n", main = "A cat")
add_phylopic_base(uuid = "23cd6aa4-9587-4a2e-8e26-de42885004c9",
                  x = 1, y = 1, ysize = 0.4)

# lots of images using a uuid
posx <- runif(10, 0, 1)
posy <- runif(10, 0, 1)
size <- runif(10, 0.1, 0.3)
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)

plot(posx, posy, type = "n", main = "A cat herd")
add_phylopic_base(uuid = "23cd6aa4-9587-4a2e-8e26-de42885004c9",
                  x = posx, y = posy, ysize = size,
                  fill = fills, angle = angle,
                  horizontal = hor, vertical = ver)

# Example using a cat background
cat <- get_phylopic("23cd6aa4-9587-4a2e-8e26-de42885004c9")
# setup plot area
plot(posx, posy, type = "n", main = "A cat herd, on top of a cat",
     xlim = c(0, 1), ylim = c(0, 1))
# plot background cat
add_phylopic_base(img = cat, alpha = 0.2)
# overlay smaller cats
add_phylopic_base(img = cat, x = posx, y = posy, ysize = size, alpha = 0.8)

## End(Not run)