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geom_phylopic.R
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geom_phylopic.R
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phylopic_env <- new.env()
#' Geom for adding PhyloPic silhouettes to a plot
#'
#' 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`).
#'
#' @details One (and only one) of the `img`, `name`, or `uuid` aesthetics must
#' be specified. The `img` aesthetic can be
#' [Picture][grImport2::Picture-class] 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.
#'
#' @section 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 `r lifecycle::badge("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()].
#'
#' @param 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.
#' @param remove_background \code{logical}. Should any white background be
#' removed from the silhouette(s)? See [recolor_phylopic()] for details.
#' @param verbose \code{logical}. Should the attribution information for the
#' used silhouette(s) be printed to the console (see [get_attribution()])?
#' @param filter \code{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.
#' @inheritParams ggplot2::layer
#' @inheritParams ggplot2::geom_point
#' @inheritParams pick_phylopic
#' @importFrom ggplot2 layer
#' @export
#' @examples \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))
#' }
geom_phylopic <- function(mapping = NULL, data = NULL,
stat = "identity", position = "identity",
...,
na.rm = FALSE,
show.legend = FALSE,
inherit.aes = TRUE,
remove_background = TRUE,
verbose = FALSE,
filter = NULL) {
if (!is.logical(remove_background)) {
stop("`remove_background` should be a logical value.")
}
if (!is.logical(verbose)) {
stop("`verbose` should be a logical value.")
}
# We need to do this before passing to the layer
dots <- list(...)
if ("img" %in% names(dots) && !is.list(dots$img)) {
dots$img <- list(dots$img)
}
if (!is.null(dots$size)) {
lifecycle::deprecate_warn("1.5.0",
I("Using the `size` aesthetic in this geom"),
I("the `height` and `width` aesthetics"),
user_env = globalenv())
if (is.null(dots$height)) {
dots$height <- dots$size
dots$size <- NULL
}
}
layer(
data = data,
mapping = mapping,
stat = stat,
geom = GeomPhylopic,
position = position,
show.legend = show.legend,
inherit.aes = inherit.aes,
params = c(
na.rm = na.rm,
remove_background = remove_background,
verbose = verbose,
filter = filter,
dots
)
)
}
#' @importFrom ggplot2 ggproto ggproto_parent Geom aes remove_missing
#' @importFrom grid gTree gList nullGrob
GeomPhylopic <- ggproto("GeomPhylopic", Geom,
required_aes = c("x", "y"),
non_missing_aes = c("alpha", "color", "fill",
"horizontal", "vertical", "angle",
"hjust", "vjust"),
optional_aes = c("height", "width", "img", "name", "uuid"),
# one and only one of img/name/uuid
# size is deprecated
default_aes = aes(height = NA, width = NA,
alpha = 1, color = NA, fill = "black",
horizontal = FALSE, vertical = FALSE, angle = 0,
hjust = 0.5, vjust = 0.5),
extra_params = c("na.rm", "remove_background", "verbose", "filter"),
setup_data = function(data, params) {
# Clean data
data <- remove_missing(data, na.rm = params$na.rm, c("img", "name", "uuid"))
if (is.list(params$filter)) params$filter <- params$filter[[1]]
# Check that only one silhouette aesthetic exists
data_cols <- sapply(c("img", "name", "uuid"),
function(col) col %in% colnames(data))
param_cols <- sapply(c("img", "name", "uuid"),
function(col) col %in% names(params))
cols <- data_cols | param_cols
if (sum(cols) != 1) {
stop(paste("Must specify one (and only one) of the `img`, `name`, or",
"`uuid` aesthetics."))
}
# Check supplied data types and retrieve silhouettes if need be
if (cols["name"]) {
if (!params$verbose) {
warning(paste("You've used the `name` aesthetic/argument. You may want",
"to use `verbose = TRUE` to get attribution information",
"for the silhouette(s)."), call. = FALSE)
}
names <- if (data_cols["name"]) data$name else params$name
if (!is.character(names)) {
stop("The `name` aesthetic should be of class character.")
}
# Get PhyloPic for each unique name
name_unique <- unique(names)
imgs <- sapply(name_unique, function(name) {
uuid <- tryCatch(get_uuid(name = name, filter = params$filter),
error = function(cond) NA)
if (is.na(uuid)) {
text <- paste0("`name` ", '"', name, '"')
if (!is.null(params$filter)) {
text <- paste0(text, " with `filter` ", '"',
paste0(params$filter, collapse = "/"), '"')
}
warning(paste0(text, " returned no PhyloPic results."), call. = FALSE)
return(NULL)
}
get_phylopic(uuid)
})
imgs <- imgs[names]
} else if (cols["uuid"]) {
uuids <- if (data_cols["uuid"]) data$uuid else params$uuid
if (!is.character(uuids)) {
stop("The `uuid` aesthetic should be of class character.")
}
# Get PhyloPic for each unique uuid
uuid_unique <- unique(uuids)
imgs <- sapply(uuid_unique, function(uuid) {
img <- tryCatch(get_phylopic(uuid),
error = function(cond) NULL)
if (is.null(img)) {
warning(paste0('"', uuid, '"', " is not a valid PhyloPic `uuid`."),
call. = FALSE)
}
img
})
imgs <- imgs[uuids]
} else {
imgs <- if (data_cols["img"]) data$img else params$img
if (any(sapply(imgs, function(img) {
!is(img, "Picture") && !is.array(img)
}))) {
stop(paste("The `img` aesthetic should be of class Picture (for a",
"vector image) or class array (for a raster image)."))
}
}
if (params$verbose && length(Filter(Negate(is.null), imgs)) > 0) {
get_attribution(img = imgs, text = TRUE)
}
data$name <- NULL
data$uuid <- NULL
data$img <- imgs
data
},
use_defaults = function(self, data, params = list(), modifiers = aes()) {
default_aes <- self$default_aes
# Inherit size as height if no height aesthetic and param exist
if (!is.null(data$size)) {
lifecycle::deprecate_warn("1.5.0",
I("Using the `size` aesthetic in this geom"),
I("the `height` and `width` aesthetics"),
user_env = globalenv())
if (is.null(data$height) && is.null(params$height)) {
data$height <- data$size
data$size <- NULL
}
}
# if fill isn't specified in the original data, copy over the colour column
col_fill <- c("colour", "fill") %in% colnames(data) |
c("colour", "fill") %in% names(params)
data <- ggproto_parent(Geom, self)$use_defaults(data, params, modifiers)
if (col_fill[1] && !col_fill[2]) {
data$fill <- data$colour
data$colour <- NA
}
data
},
draw_panel = function(self, data, panel_params, coord, na.rm = FALSE,
remove_background = TRUE, filter = NULL) {
phylopic_env$remove_background <- remove_background
# reset the legend key index (since the panel is plotted after the legend)
phylopic_env$glyph_ind <- 1
# Check that aesthetics are valid
if (any(data$alpha > 1 | data$alpha < 0)) {
stop("`alpha` must be between 0 and 1.")
}
if (any(data$hjust > 1 | data$hjust < 0)) {
stop("`hjust` must be between 0 and 1.")
}
if (any(data$vjust > 1 | data$vjust < 0)) {
stop("`vjust` must be between 0 and 1.")
}
if (!is.null(data$size)) {
lifecycle::deprecate_warn("1.5.0",
I("Using the `size` aesthetic in this geom"),
I("the `height` and `width` aesthetics"),
user_env = globalenv())
if (is.null(data$height) && is.null(params$height)) {
data$height <- data$size
data$size <- NULL
}
}
if (any(!is.na(data$height) & !is.na(data$width))) {
stop("At least one of `height` or `width` must be NA.")
}
# Transform data
data <- coord$transform(data, panel_params)
if (any(!is.na(data$height))) {
# Calculate height as percentage of y limits
# (or r limits for polar coordinates)
if ("y.range" %in% names(panel_params)) {
y_diff <- diff(panel_params$y.range)
} else if ("y_range" %in% names(panel_params)) { # exclusive to coord_sf
y_diff <- diff(panel_params$y_range)
} else if ("r.range" %in% names(panel_params)) { # exclusive to coord_polar
y_diff <- diff(panel_params$r.range)
} else {
y_diff <- 1
}
if (any(data$height < (y_diff / 1000), na.rm = TRUE)) {
warning(paste("Your specified silhouette `height`(s) are more than",
"1000 times smaller than your y-axis range. You probably",
"want to use a larger `height`."), call. = FALSE)
}
data$height <- data$height / y_diff
}
if (any(!is.na(data$width))) {
# Calculate width as percentage of x limits
# (or r limits for polar coordinates)
if ("x.range" %in% names(panel_params)) {
x_diff <- diff(panel_params$x.range)
} else if ("x_range" %in% names(panel_params)) { # exclusive to coord_sf
x_diff <- diff(panel_params$x_range)
} else if ("r.range" %in% names(panel_params)) { # exclusive to coord_polar
x_diff <- diff(panel_params$r.range)
} else {
x_diff <- 1
}
if (any(data$width < (x_diff / 1000), na.rm = TRUE)) {
warning(paste("Your specified silhouette `width`(s) are more than 1000",
"times smaller than your x-axis range. You probably want",
"to use a larger `width`."), call. = FALSE)
}
data$width <- data$width / x_diff
}
# Make a grob for each silhouette
grobs <- lapply(seq_len(nrow(data)), function(i) {
if (is.null(data$img[[i]])) {
nullGrob()
} else {
phylopicGrob(data$img[[i]], data$x[i], data$y[i],
data$height[i], data$width[i],
data$colour[i], data$fill[i], data$alpha[i],
data$horizontal[i], data$vertical[i], data$angle[i],
data$hjust[i], data$vjust[i],
remove_background)
}
})
# Return the grobs as a gTree
ggname("geom_phylopic", gTree(children = do.call(gList, grobs)))
}
)
phylopic_env$glyph_ind <- 1
#' Use PhyloPics as legend key glyphs
#'
#' Specify existing images, taxonomic names, or PhyloPic uuids to use PhyloPic
#' silhouettes as legend key glyphs in a ggplot plot.
#'
#' @param img A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param name \code{character}. A taxonomic name to be passed to [get_uuid()].
#' @param uuid \code{character}. A valid uuid for a PhyloPic silhouette (such as
#' that returned by [get_uuid()] or [pick_phylopic()]).
#' @details One (and only one) of `img`, `name`, or `uuid` must be specified.
#'
#' This argument may also be a vector/list of valid values if multiple
#' silhouettes should be used as key glyphs. In this case, the specified
#' silhouettes will be used as ordered as key glyphs one by one, with
#' recycling as necessary.
#'
#' Note that the sizes of the silhouettes in the legend are currently
#' maximized based on the size of the key. This size can be modified using the
#' `legend.key.size` argument in [ggplot2::theme()]. Therefore, the
#' silhouettes will not reflect the size aesthetic, and this function should
#' not be used for size legends.
#' @importFrom grid nullGrob unit
#' @export
#' @examples
#' \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, color = name), size = 10,
#' show.legend = TRUE,
#' key_glyph = phylopic_key_glyph(name =
#' c("Felis silvestris catus",
#' "Odobenus rosmarus"))) +
#' coord_cartesian(xlim = c(1,6), ylim = c(5, 30))
#' }
phylopic_key_glyph <- function(img = NULL, name = NULL, uuid = NULL) {
if (sum(sapply(list(img, name, uuid), Negate(is.null))) != 1) {
stop(paste("Must specify one (and only one) of the `img`, `name`, or",
"`uuid` arguments"))
}
if (!is.null(name)) {
if (!is.character(name)) {
stop("`name` should be of class character.")
}
# Get PhyloPic for each unique name
name_unique <- unique(name)
imgs <- sapply(name_unique, function(x) {
url <- tryCatch(get_uuid(name = x, url = TRUE),
error = function(cond) NA)
if (is.na(url)) {
warning(paste0("`name` ", '"', x, '"',
" returned no PhyloPic results."))
return(NULL)
}
get_svg(url)
})
imgs <- imgs[name]
} else if (!is.null(uuid)) {
if (!is.character(uuid)) {
stop("`uuid` should be of class character.")
}
# Get PhyloPic for each unique uuid
uuid_unique <- unique(uuid)
imgs <- sapply(uuid_unique, function(x) {
img <- tryCatch(get_phylopic(x),
error = function(cond) NULL)
if (is.null(img)) {
warning(paste0('"', x, '"', " is not a valid PhyloPic `uuid`."))
}
img
})
imgs <- imgs[uuid]
} else {
if (!is.list(img)) img <- list(img)
if (any(sapply(img, function(x) {
!is(x, "Picture") && !is.array(x)
}))) {
stop(paste("`img` should be of class Picture (for a vector image)",
"or class array (for a raster image)."))
}
imgs <- img
}
function(data, params, size) {
i <- phylopic_env$glyph_ind
if (is.null(imgs[[i]])) {
grob <- nullGrob()
} else {
asp_rat <- aspect_ratio(imgs[[i]])
height <- unit(ifelse(asp_rat >= 1, .95 / asp_rat, .95), "npc")
grob <- phylopicGrob(imgs[[i]], x = 0.5, y = 0.5,
height, width = unit(1, "npc"),
data$colour[1], data$fill[1], data$alpha[1],
data$horizontal[1], data$vertical[1], data$angle[1],
hjust = 0.5, vjust = 0.5,
phylopic_env$remove_background)
}
if (i == length(imgs)) {
phylopic_env$glyph_ind <- 1
} else {
phylopic_env$glyph_ind <- phylopic_env$glyph_ind + 1
}
grob
}
}
#' @importFrom grImport2 pictureGrob
#' @importFrom grid rasterGrob gList gTree nullGrob
#' @importFrom methods slotNames
phylopicGrob <- function(img, x, y, height, width,
color, fill, alpha,
horizontal, vertical, angle,
hjust, vjust,
remove_background) {
if (horizontal || vertical) img <- flip_phylopic(img, horizontal, vertical)
if (!is.na(angle) && angle != 0) img <- rotate_phylopic(img, angle)
# recolor if necessary
color <- if (is.na(color) || color == "original") NULL else color
if (is.na(fill)) fill <- color
fill <- if (!is.null(fill) && fill == "original") NULL else fill
img <- recolor_phylopic(img, alpha, color, fill, remove_background)
# convert NAs to NULLs
if (is.na(height)) height <- NULL
if (is.na(width)) width <- NULL
# grobify
if (is(img, "Picture")) { # svg
if ("summary" %in% slotNames(img) &&
all(c("xscale", "yscale") %in% slotNames(img@summary)) &&
is.numeric(img@summary@xscale) && length(img@summary@xscale) == 2 &&
all(is.finite(img@summary@xscale)) && diff(img@summary@xscale) != 0 &&
is.numeric(img@summary@yscale) && length(img@summary@yscale) == 2 &&
all(is.finite(img@summary@yscale)) && diff(img@summary@yscale) != 0) {
# modified from
# https://github.com/k-hench/hypoimg/blob/master/R/hypoimg_recolor_svg.R
img_grob <- pictureGrob(img, x = x, y = y,
height = height, width = width,
default.units = "native", expansion = 0,
hjust = hjust, vjust = vjust,
delayContent = TRUE)
img_grob <- gList(img_grob)
img_grob <- gTree(children = img_grob)
} else {
img_grob <- nullGrob()
}
} else { # png
img_grob <- rasterGrob(img, x = x, y = y,
height = height, width = width,
default.units = "native",
hjust = hjust, vjust = vjust)
}
return(img_grob)
}
#' Scales for phylopic height or width
#'
#' `scale_height_continuous()` scales the height of silhouettes whereas
#' `scale_width_continuous()` scales the height of silhouettes.
#' @inheritParams ggplot2::scale_size_continuous
#' @export
#' @importFrom ggplot2 continuous_scale waiver
#' @importFrom scales pal_area
#' @rdname scales
scale_height_continuous <- function(name = waiver(), breaks = waiver(), labels = waiver(),
limits = NULL, range = c(1, 6),
transform = "identity",
trans = lifecycle::deprecated(),
guide = "none") {
continuous_scale("height", palette = scales::pal_area(range), name = name,
breaks = breaks, labels = labels, limits = limits,
transform = transform, trans = trans, guide = guide)
}
#' @inheritParams ggplot2::scale_size_continuous
#' @export
#' @importFrom ggplot2 continuous_scale waiver
#' @importFrom scales pal_area
#' @rdname scales
scale_width_continuous <- function(name = waiver(), breaks = waiver(), labels = waiver(),
limits = NULL, range = c(1, 6),
transform = "identity",
trans = lifecycle::deprecated(),
guide = "none") {
continuous_scale("width", palette = scales::pal_area(range), name = name,
breaks = breaks, labels = labels, limits = limits,
transform = transform, trans = trans, guide = guide)
}
#' @importFrom grid grobName
ggname <- function(prefix, grob) {
# copied from ggplot2
grob$name <- grobName(grob, prefix)
grob
}
aspect_ratio <- function(img) {
if (is(img, "Picture")) {
return(abs(diff(img@summary@xscale)) / abs(diff(img@summary@yscale)))
} else {
dims <- dim(img)
return(dims[2] / dims[1])
}
}