-
Notifications
You must be signed in to change notification settings - Fork 9
/
phylopic_utils.R
338 lines (316 loc) · 11.2 KB
/
phylopic_utils.R
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
#' Flip a PhyloPic silhouette along its horizontal and/or vertical axis
#'
#' The picture can be a [Picture][grImport2::Picture-class] or png array object,
#' e.g., from using [get_phylopic()].
#'
#' @param img A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param horizontal \code{logical}. Should the silhouette be flipped
#' horizontally?
#' @param vertical \code{logical}. Should the silhouette be flipped vertically?
#' @return A [Picture][grImport2::Picture-class] or png array object (matching
#' the type of `img`)
#' @family transformations
#' @export
flip_phylopic <- function(img, horizontal = TRUE, vertical = FALSE) {
if (!is.logical(horizontal)) stop("`horizontal` must be TRUE or FALSE.")
if (!is.logical(vertical)) stop("`vertical` must be TRUE or FALSE.")
UseMethod("flip_phylopic")
}
#' @export
flip_phylopic.Picture <- function(img, horizontal = TRUE, vertical = FALSE) {
# modified from
# https://github.com/thomasp85/ggforce/blob/main/R/trans_linear.R
if (horizontal) {
mat <- matrix(c(-1, 0, 0,
0, 1, 0,
0, 0, 1), ncol = 3, byrow = TRUE)
img <- transform_picture(img, mat)
}
if (vertical) {
mat <- matrix(c(1, 0, 0,
0, -1, 0,
0, 0, 1), ncol = 3, byrow = TRUE)
img <- transform_picture(img, mat)
}
img
}
#' @export
flip_phylopic.array <- function(img, horizontal = TRUE, vertical = FALSE) {
cls <- class(img)
if (length(dim(img)) != 3) {
stop("`img` must be an array with three dimensions.")
}
# modified from https://github.com/richfitz/vectoR/blob/master/R/vector.R
if (horizontal) {
img <- img[, rev(seq_len(ncol(img))), , drop = FALSE]
}
if (vertical) {
img <- img[rev(seq_len(nrow(img))), , , drop = FALSE]
}
class(img) <- cls
img
}
#' Rotate a PhyloPic silhouette
#'
#' The picture can be a [Picture][grImport2::Picture-class] or png array object,
#' e.g., from using [get_phylopic()]. Note that png array objects can only be
#' rotated by multiples of 90 degrees.
#'
#' @param img A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param angle \code{numeric}. The number of degrees to rotate the silhouette
#' clockwise.
#' @return A [Picture][grImport2::Picture-class] or png array object (matching
#' the type of `img`)
#' @family transformations
#' @export
rotate_phylopic <- function(img, angle = 90) {
if (!is.numeric(angle)) stop("`angle` must be a number.")
UseMethod("rotate_phylopic")
}
#' @export
rotate_phylopic.Picture <- function(img, angle = 90) {
# change to radians
angle <- angle / 360 * (2 * pi)
# change to clockwise
angle <- (2 * pi) - angle
# create rotation matrix (modified from
# https://github.com/thomasp85/ggforce/blob/main/R/trans_linear.R)
mat <- matrix(c(cos(angle), sin(angle), 0,
-sin(angle), cos(angle), 0,
0, 0, 1), ncol = 3, byrow = TRUE)
transform_picture(img, mat)
}
#' @export
rotate_phylopic.array <- function(img, angle = 90) {
if (length(dim(img)) != 3) {
stop("`img` must be an array with three dimensions.")
}
if (angle %% 90 != 0) {
stop(paste("`angle` must be divisible by 90. Other angles are not yet",
"implemented for rasterized PhyloPics."))
}
# modified from https://stackoverflow.com/a/16497058/4660582
if (angle > 0) { # clockwise
rotate <- function(mat) t(mat[rev(seq_len(nrow(mat))), , drop = FALSE])
} else if (angle < 0) { # counter clockwise
rotate <- function(mat) {
mat_t <- t(mat)
mat_t[rev(seq_len(nrow(mat_t))), , drop = FALSE]
}
}
img_new <- img
for (i in seq_len(abs(angle) / 90)) {
img_new <- simplify2array(
lapply(seq_len(dim(img_new)[3]),
function(i) rotate(img_new[, , i]))
)
}
class(img_new) <- class(img)
img_new
}
#' @importFrom grImport2 applyTransform
transform_picture <- function(img, mat) {
# transform the img content given the specified transformation matrix
img@content <- lapply(img@content, function(cont) applyTransform(cont, mat))
# transform the xscale and yscale with the same matrix
img@summary <- transform_summary(img@summary, mat)
img
}
transform_summary <- function(summary, mat) {
# transform the corners given the specified transformation matrix
corners <- expand.grid(x = summary@xscale, y = summary@yscale)
corners_trans <- mat %*% rbind(corners$x, corners$y, z = 1)
# maintain the directionality of the scales
rev_x <- summary@xscale[1] > summary@xscale[2]
rev_y <- summary@yscale[1] > summary@yscale[2]
# set the new scales
summary@xscale <- range(corners_trans[1, ])
if (rev_x) summary@xscale <- rev(summary@xscale)
summary@yscale <- range(corners_trans[2, ])
if (rev_y) summary@yscale <- rev(summary@yscale)
summary
}
#' Recolor a PhyloPic image
#'
#' Function to recolor and change alpha levels of a PhyloPic image.
#'
#' @param img A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param alpha \code{numeric}. A value between 0 and 1, specifying the opacity
#' of the silhouette.
#' @param color \code{character}. Color to make the outline of the silhouette.
#' If NULL, the outline color is not changed.
#' @param fill \code{character}. Color to make the body of the silhouette. If
#' NULL, the body color is not changed.
#' @param remove_background \code{logical}. Should any white background be
#' removed? Only useful if `img` is a [Picture][grImport2::Picture-class]
#' object. See details.
#'
#' @details Some PhyloPic silhouettes do not have a transparent background.
#' Consequently, when color is used with vectorized versions of these images,
#' the entire image--including the background--is recolored. Setting
#' `remove_background` to `TRUE` (the default) will remove any white parts of
#' the image (which should only be the background).
#'
#' @return A [Picture][grImport2::Picture-class] or png array object (matching
#' the type of `img`)
#' @family transformations
#' @importFrom grDevices rgb col2rgb
#' @export
recolor_phylopic <- function(img, alpha = 1, color = NULL, fill = NULL,
remove_background = TRUE) {
if (!is.numeric(alpha) || alpha < 0 || alpha > 1) {
stop("`alpha` must be a number between 0 and 1.")
}
if (!is.character(color) && !is.null(color)) {
stop("`color` must be a character value.")
}
UseMethod("recolor_phylopic")
}
#' @export
recolor_phylopic.array <- function(img, alpha = 1, color = NULL, fill = NULL,
remove_background = TRUE) {
cls <- class(img)
if (!is.null(color)) {
message("Outline color does not currently work with png image objects.")
}
dims <- dim(img)
if (length(dim(img)) != 3) {
stop("`img` must be an array with three dimensions.")
}
# convert to RGBA if needed
if (dims[3] == 1) { # grayscale
img <- g_to_rgba(img)
} else if (dims[3] == 2) { # greyscale and alpha
img <- ga_to_rgba(img)
} else if (dims[3] == 3) { # RGB
img <- rgb_to_rgba(img)
} else if (dims[3] > 4) { # not supported
stop(paste("`img` must be in G, GA, RGB, or RGBA format.",
"More than four channels is not supported."))
}
dims <- dim(img) # update dimensions
if (is.null(fill)) {
new_img <- array(c(img[, , 1:3], img[, , 4] * alpha), dim = dims)
} else {
cols <- col2rgb(fill) / 255
imglen <- length(img[, , 1])
new_img <- array(c(rep(cols[1, 1], imglen),
rep(cols[2, 1], imglen),
rep(cols[3, 1], imglen),
img[, , 4] * alpha), dim = dims)
}
class(new_img) <- cls
return(new_img)
}
ga_to_rgba <- function(img) {
new_img <- array(0, dim = c(dim(img)[1:2], 4))
new_img[, , 4] <- img[, , 2]
new_img
}
g_to_rgba <- function(img) {
new_img <- array(0, dim = c(dim(img)[1:2], 2))
new_img[, , 2] <- img
ga_to_rgba(new_img)
}
rgb_to_rgba <- function(img) {
new_img <- array(0, dim = c(dim(img)[1:2], 4))
new_img[, , 1:3] <- img[, , 1:3]
new_img[, , 4] <- 1
new_img
}
#' @export
recolor_phylopic.Picture <- function(img, alpha = 1, color = NULL, fill = NULL,
remove_background = TRUE) {
img <- recolor_content(img, alpha, color, fill, remove_background)
if (length(img@content) == 0) stop("Invalid 'Picture' object")
return(img)
}
#' @importFrom methods slotNames
recolor_content <- function(x, alpha, color, fill, remove_background) {
tmp <- lapply(x@content, function(element) {
if (is(element, "PicturePath")) {
# a bit of a hack until PhyloPic fixes these white backgrounds
if (remove_background && "gp" %in% slotNames(element) &&
"fill" %in% names(element@gp) &&
element@gp$fill %in% c("#FFFFFFFF", "#FFFFFF")) {
return(NULL)
} else {
element@gp$alpha <- alpha
if (!is.null(color)) {
element@gp$col <- color
}
if (!is.null(fill)) {
element@gp$fill <- fill
}
return(element)
}
} else if (is(element, "PictureGroup")) {
# need to go another level down
recolor_content(element, alpha, color, fill, remove_background)
}
})
x@content <- Filter(function(element) !is.null(element), tmp)
return(x)
}
#' Preview a PhyloPic silhouette
#'
#' Preview a raster or vector representation of a PhyloPic silhouette. This will
#' plot the silhouette on a new page in your default plotting device.
#' @rdname plot_phylopic
#' @aliases plot_phylopic
#' @param x A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param ... Other arguments passed on to [grImport2::grid.picture()] or
#' [grid::grid.raster()].
#' @importFrom grid grid.newpage
#' @importFrom grImport2 grid.picture
#' @export
plot.Picture <- function(x, ...) {
args <- list(...)
if (is.null(args$expansion)) args$expansion <- 0
if (is.null(args$delayContent)) args$delayContent <- TRUE
args$picture <- x
grid.newpage()
do.call(grid.picture, args)
}
#' @rdname plot_phylopic
#' @importFrom grid grid.newpage grid.raster
#' @export
plot.phylopic <- function(x, ...) {
grid.newpage()
grid.raster(x, ...)
}
#' @rdname get_phylopic
#' @param x A [Picture][grImport2::Picture-class] or png array object, e.g.,
#' from using [get_phylopic()].
#' @param ... Ignored
#' @export
print.Picture <- function(x, ...) {
dims <- c(abs(diff(x@summary@xscale)), abs(diff(x@summary@yscale)))
cat(paste0("PhyloPic silhouette object (vector format)",
"\nDimensions: ", dims[1], " pixels wide and ",
dims[2], " pixels tall",
"\nuuid: ", attr(x, "uuid"),
"\nURL: ", attr(x, "url")))
invisible(x)
}
# runs print() when you just type the object name (S4-specific)
setMethod(f = "show",
signature = "Picture",
definition = function(object) {
print(object)
})
#' @rdname get_phylopic
#' @export
print.phylopic <- function(x, ...) {
dims <- dim(x)
cat(paste0("PhyloPic silhouette object (raster format)",
"\nDimensions: ", dims[2], " pixels wide and ",
dims[1], " pixels tall",
"\nuuid: ", attr(x, "uuid"),
"\nURL: ", attr(x, "url")))
invisible(x)
}