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(v2.1.1.9186) replace antibiotics with antimicrobials!

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dr. M.S. (Matthijs) Berends
2025-03-07 20:43:26 +01:00
parent f2b2a450cb
commit f7938289eb
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158
tests/testthat/test-plotting.R
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@ -27,88 +27,90 @@
# how to conduct AMR data analysis: https://msberends.github.io/AMR/ #
# ==================================================================== #
if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
pdf(NULL) # prevent Rplots.pdf being created
test_that("plotting works", {
if (AMR:::pkg_is_available("ggplot2", also_load = TRUE)) {
pdf(NULL) # prevent Rplots.pdf being created
# scale_*_mic
aesthetics <- c("x", "y", "colour", "fill")
expected_methods <- c("transform", "transform_df", "breaks", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- paste0("scale_", aest, "_continuous")
scale_obj <- getExportedValue("ggplot2", scale_fn_name)()
# scale_*_mic
aesthetics <- c("x", "y", "colour", "fill")
expected_methods <- c("transform", "transform_df", "breaks", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- paste0("scale_", aest, "_continuous")
scale_obj <- getExportedValue("ggplot2", scale_fn_name)()
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
)
}
}
# scale_*_sir
aesthetics <- c("colour", "fill")
expected_methods <- c("transform", "transform_df", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- "scale_discrete_manual"
scale_obj <- getExportedValue("ggplot2", scale_fn_name)(aesthetics = aest)
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
)
}
}
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
expect_true(is.function(ggplot2::scale_x_discrete()[[method]]) || method %in% names(ggplot2::scale_x_discrete()),
info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete")
)
}
}
# scale_*_sir
aesthetics <- c("colour", "fill")
expected_methods <- c("transform", "transform_df", "labels", "limits")
for (aest in aesthetics) {
scale_fn_name <- "scale_discrete_manual"
scale_obj <- getExportedValue("ggplot2", scale_fn_name)(aesthetics = aest)
for (method in expected_methods) {
expect_true(is.function(scale_obj[[method]]) || method %in% names(scale_obj),
info = paste0("Method '", method, "' is missing in ggplot2::", scale_fn_name)
)
}
}
for (method in expected_methods) {
expect_true(is.function(ggplot2::scale_x_discrete()[[method]]) || method %in% names(ggplot2::scale_x_discrete()),
info = paste0("Method '", method, "' is missing in ggplot2::", "scale_x_discrete")
expect_inherits(
ggplot(
data.frame(
count = c(1, 2, 3, 4),
sir = c("S", "I", "R", "SDD")
),
aes(x = sir, y = count, fill = sir)
) +
geom_col() +
scale_x_sir(eucast_I = F, language = "el") +
scale_fill_sir(eucast_I = T, language = "nl"),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_point() +
scale_y_mic(),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_col() +
scale_y_mic(),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_col() +
scale_y_mic(mic_range = c(4, 16)) +
scale_x_sir(),
"gg"
)
}
expect_inherits(
ggplot(
data.frame(
count = c(1, 2, 3, 4),
sir = c("S", "I", "R", "SDD")
),
aes(x = sir, y = count, fill = sir)
) +
geom_col() +
scale_x_sir(eucast_I = F, language = "el") +
scale_fill_sir(eucast_I = T, language = "nl"),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_point() +
scale_y_mic(),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_col() +
scale_y_mic(),
"gg"
)
expect_inherits(
ggplot(
data.frame(
mic = as.mic(c(2, 4, 8, 16)),
sir = as.sir(c("S", "I", "R", "SDD"))
),
aes(x = sir, y = mic)
) +
geom_col() +
scale_y_mic(mic_range = c(4, 16)) +
scale_x_sir(),
"gg"
)
}
})