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Geom for adding PhyloPic silhouettes to a plot

Source: R/geom_phylopic.R
geom_phylopic.Rd

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. When using a geom_*() function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

  • For more information and other ways to specify the stat, see the layer stat documentation.

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

  • For more information and other ways to specify the position, see the layer position documentation.

...

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

  • Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

  • When constructing a layer using a stat_*() function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

  • Inversely, when constructing a layer using a geom_*() function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

  • The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

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 height or width aesthetic specifies the height or width, respectively, of the silhouettes in the units of the y axis (only one is allowed). The aspect ratio of the silhouettes will always be maintained. The hjust and vjust aesthetics can be used to manage the justification of the silhouettes with respect to the x and y coordinates.

The color (default: NA), fill (default: "black"), 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 color will be used as the fill color (for backwards compatibility). 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"). To remove the fill or outline, you can set fill or color to "transparent", respectively.

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 or uuid or name (one, and only one, required)

  • height or width (optional, maximum of only one allowed)

  • ysize [Deprecated] Deprecated in favor of height or width

  • color or colour

  • fill

  • alpha

  • horizontal

  • vertical

  • angle

  • hjust

  • vjust

    Learn more about setting these aesthetics in add_phylopic().

Examples

if (FALSE) { # \dontrun{
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),
                fill = "purple", height = 10) +
  facet_wrap(~name) +
  coord_cartesian(xlim = c(1,6), ylim = c(5, 30))
} # }