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Fix color/fill defaults and behavior #91

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merged 5 commits into from
Nov 20, 2023
Merged

Fix color/fill defaults and behavior #91

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6c97cbc
Change color/fill defaults and behavior when only color is specified;…
willgearty Nov 16, 2023
0e6f17d
update NEWS.md
willgearty Nov 16, 2023
3470a77
Add walrus glyph to test
willgearty Nov 20, 2023
490a5b1
Fix defaults
willgearty Nov 20, 2023
ad4dbc4
Add text about "transparent"
willgearty Nov 20, 2023
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1 change: 1 addition & 0 deletions NEWS.md
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Original file line number Diff line number Diff line change
Expand Up @@ -2,6 +2,7 @@

* updated citation
* added warning when specified size is more than 1000 times smaller than the y-axis range (mostly useful for when making maps with coord_sf) (#86)
* changed the defaults and behavior of the color and fill argument/aesthetics to better maintain backwards compatibility but also prevent unnecessary outlines (#87)

# rphylopic 1.2.2

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14 changes: 8 additions & 6 deletions R/add_phylopic.r
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Expand Up @@ -21,11 +21,13 @@
#' of the silhouette (0 is fully transparent, 1 is fully opaque).
#' @param color \code{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").
#' (usually the same as "transparent"). To remove the outline, you can set
#' this to "transparent".
#' @param fill \code{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 the outline and
#' fill color will be the same.
#' 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".
#' @param horizontal \code{logical}. Should the silhouette be flipped
#' horizontally?
#' @param vertical \code{logical}. Should the silhouette be flipped vertically?
Expand Down Expand Up @@ -68,20 +70,20 @@
#' angle <- runif(10, 0, 360)
#' hor <- sample(c(TRUE, FALSE), 10, TRUE)
#' ver <- sample(c(TRUE, FALSE), 10, TRUE)
#' cols <- sample(c("black", "darkorange", "grey42", "white"), 10,
#' 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, ysize = sizey,
#' color = cols, alpha = alpha, angle = angle,
#' fill = fills, alpha = alpha, angle = angle,
#' horizontal = hor, vertical = ver)
#' p + ggtitle("R Cat Herd!!")
add_phylopic <- function(img = NULL, name = NULL, uuid = NULL, filter = NULL,
x, y, ysize = Inf,
alpha = 1, color = "black", fill = NA,
alpha = 1, color = NA, fill = "black",
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This doesn't seem to be consistent with add_phylopic_base?

horizontal = FALSE, vertical = FALSE, angle = 0,
remove_background = TRUE, verbose = FALSE) {
if (all(sapply(list(img, name, uuid), is.null))) {
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23 changes: 14 additions & 9 deletions R/add_phylopic_base.r
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Expand Up @@ -23,11 +23,13 @@
#' of the silhouette (0 is fully transparent, 1 is fully opaque).
#' @param color \code{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").
#' (usually the same as "transparent"). To remove the outline, you can set
#' this to "transparent".
#' @param fill \code{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 the outline and
#' fill color will be the same.
#' 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".
#' @param horizontal \code{logical}. Should the silhouette be flipped
#' horizontally?
#' @param vertical \code{logical}. Should the silhouette be flipped vertically?
Expand Down Expand Up @@ -75,13 +77,13 @@
#' angle <- runif(10, 0, 360)
#' hor <- sample(c(TRUE, FALSE), 10, TRUE)
#' ver <- sample(c(TRUE, FALSE), 10, TRUE)
#' cols <- sample(c("black", "darkorange", "grey42", "white"), 10,
#' 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,
#' color = cols, angle = angle,
#' fill = fills, angle = angle,
#' horizontal = hor, vertical = ver)
#'
#' # Example using a cat background
Expand All @@ -93,10 +95,10 @@
#' 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)
add_phylopic_base <- function(img = NULL, name = NULL, uuid = NULL,

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file=R/add_phylopic_base.r,line=98,col=1,[cyclocomp_linter] Functions should have cyclomatic complexity of less than 15, this has 91.
filter = NULL,
x = NULL, y = NULL, ysize = NULL,
alpha = 1, color = "black", fill = NA,
alpha = 1, color = NA, fill = "black",
horizontal = FALSE, vertical = FALSE, angle = 0,
remove_background = TRUE, verbose = FALSE) {
if (all(sapply(list(img, name, uuid), is.null))) {
Expand Down Expand Up @@ -190,15 +192,18 @@
if (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 (fill == "original") NULL else fill
if (is.na(color) || color == "original") color <- NULL
if (is.na(fill)) {
fill <- color
color <- NULL

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}
if (fill == "original") fill <- NULL

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img <- recolor_phylopic(img, alpha, color, fill, remove_background)

# grobify and plot
if (is(img, "Picture")) { # svg
if ("summary" %in% slotNames(img) &&
all(c("xscale", "yscale") %in% slotNames(img@summary)) &&

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file=R/add_phylopic_base.r,line=206,col=10,[indentation_linter] Indentation should be 12 spaces but is 10 spaces.
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 &&
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27 changes: 14 additions & 13 deletions R/geom_phylopic.R
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Expand Up @@ -14,15 +14,16 @@
#' specifies the height of the silhouettes in the units of the y axis. The
#' aspect ratio of the silhouettes will always be maintained.
#'
#' The `color` (default: "black"), `fill` (default: NA), 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 the outline and fill color will be
#' the same. 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").
#' The `color` (default: NA), `fill` (default: "black"), and `alpha` (
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I am not sure this is working as expected, e.g.

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 = NA, size = 10) +
  facet_wrap(~name) +
  coord_cartesian(xlim = c(1,6), ylim = c(5, 30))

image

#' 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
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Again, I am not sure this is behaving as expected:

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 = NA, color = "blue", size = 10) +
  facet_wrap(~name) +
  coord_cartesian(xlim = c(1,6), ylim = c(5, 30))

image

#' 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.
Expand Down Expand Up @@ -74,16 +75,16 @@
#' name = c("Felis silvestris catus", "Odobenus rosmarus"))
#' ggplot(df) +
#' geom_phylopic(aes(x = x, y = y, name = name),
#' color = "purple", size = 10) +
#' fill = "purple", size = 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,

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show.legend = FALSE,

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file=R/geom_phylopic.R,line=86,col=27,[object_name_linter] Variable and function name style should match snake_case or symbols.
inherit.aes = TRUE,

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file=R/geom_phylopic.R,line=87,col=27,[object_name_linter] Variable and function name style should match snake_case or symbols.
remove_background = TRUE,
verbose = FALSE,
filter = NULL) {
Expand Down Expand Up @@ -118,13 +119,12 @@

#' @importFrom ggplot2 ggproto ggproto_parent Geom aes remove_missing
#' @importFrom grid gTree gList nullGrob
GeomPhylopic <- ggproto("GeomPhylopic", Geom,

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file=R/geom_phylopic.R,line=122,col=1,[object_name_linter] Variable and function name style should match snake_case or symbols.
required_aes = c("x", "y"),
non_missing_aes = c("size", "alpha", "color",
non_missing_aes = c("size", "alpha", "color", "fill",
"horizontal", "vertical", "angle"),
optional_aes = c("img", "name", "uuid"), # one and only one of these
default_aes = aes(size = 6, alpha = 1,
color = "black", fill = NA,
default_aes = aes(size = 6, alpha = 1, color = NA, fill = "black",
horizontal = FALSE, vertical = FALSE, angle = 0),
extra_params = c("na.rm", "remove_background", "verbose", "filter"),
setup_data = function(data, params) {
Expand Down Expand Up @@ -212,10 +212,11 @@
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,

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remove_background = TRUE, filter = NULL) {
phylopic_env$remove_background <- remove_background
# reset the legend key index (since the panel is plotted after the legend)
Expand Down Expand Up @@ -377,7 +378,7 @@
#' @importFrom grImport2 pictureGrob
#' @importFrom grid rasterGrob gList gTree nullGrob
#' @importFrom methods slotNames
phylopicGrob <- function(img, x, y, height, color, fill, alpha,

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horizontal, vertical, angle,
remove_background) {
# modified from add_phylopic for now
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16 changes: 9 additions & 7 deletions man/add_phylopic.Rd
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16 changes: 9 additions & 7 deletions man/add_phylopic_base.Rd
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27 changes: 13 additions & 14 deletions man/geom_phylopic.Rd
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30 changes: 15 additions & 15 deletions tests/testthat/_snaps/add_phylopic/phylopic-in-background.svg
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