mirror of
https://github.com/msberends/AMR.git
synced 2025-07-10 14:21:48 +02:00
(v2.1.1.9118) move ggplot2 plotting functions to general 'plotting' man page
This commit is contained in:
201
R/ggplot_sir.R
201
R/ggplot_sir.R
@ -52,18 +52,15 @@
|
||||
#' @param ... other arguments passed on to [geom_sir()] or, in case of [scale_sir_colours()], named values to set colours. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red. See *Examples*.
|
||||
#' @details At default, the names of antibiotics will be shown on the plots using [ab_name()]. This can be set with the `translate_ab` argument. See [count_df()].
|
||||
#'
|
||||
#' ### The Functions
|
||||
#' [geom_sir()] will take any variable from the data that has an [`sir`] class (created with [as.sir()]) using [sir_df()] and will plot bars with the percentage S, I, and R. The default behaviour is to have the bars stacked and to have the different antibiotics on the x axis.
|
||||
#'
|
||||
#' Additional functions include:
|
||||
#'
|
||||
#' [facet_sir()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
|
||||
#'
|
||||
#' [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
|
||||
#'
|
||||
#' [scale_sir_colours()] sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
|
||||
#'
|
||||
#' [theme_sir()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
|
||||
#'
|
||||
#' [labels_sir_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
|
||||
#' * [facet_sir()] creates 2d plots (at default based on S/I/R) using [ggplot2::facet_wrap()].
|
||||
#' * [scale_y_percent()] transforms the y axis to a 0 to 100% range using [ggplot2::scale_y_continuous()].
|
||||
#' * [scale_sir_colours()] sets colours to the bars (green for S, yellow for I, and red for R). with multilingual support. The default colours are colour-blind friendly, while maintaining the convention that e.g. 'susceptible' should be green and 'resistant' should be red.
|
||||
#' * [theme_sir()] is a [ggplot2 theme][[ggplot2::theme()] with minimal distraction.
|
||||
#' * [labels_sir_count()] print datalabels on the bars with percentage and amount of isolates using [ggplot2::geom_text()].
|
||||
#'
|
||||
#' [ggplot_sir()] is a wrapper around all above functions that uses data as first input. This makes it possible to use this function after a pipe (`%>%`). See *Examples*.
|
||||
#' @rdname ggplot_sir
|
||||
@ -344,187 +341,3 @@ geom_sir <- function(position = NULL,
|
||||
...
|
||||
)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_sir
|
||||
#' @export
|
||||
facet_sir <- function(facet = c("interpretation", "antibiotic"), nrow = NULL) {
|
||||
facet <- facet[1]
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(facet, allow_class = "character", has_length = 1)
|
||||
meet_criteria(nrow, allow_class = c("numeric", "integer"), has_length = 1, allow_NULL = TRUE, is_positive = TRUE, is_finite = TRUE)
|
||||
|
||||
# we work with aes_string later on
|
||||
facet_deparse <- deparse(substitute(facet))
|
||||
if (facet_deparse != "facet") {
|
||||
facet <- facet_deparse
|
||||
}
|
||||
if (facet %like% '".*"') {
|
||||
facet <- substr(facet, 2, nchar(facet) - 1)
|
||||
}
|
||||
|
||||
if (tolower(facet) %in% tolower(c("SIR", "sir", "interpretations", "result"))) {
|
||||
facet <- "interpretation"
|
||||
} else if (tolower(facet) %in% tolower(c("ab", "abx", "antibiotics"))) {
|
||||
facet <- "antibiotic"
|
||||
}
|
||||
|
||||
ggplot2::facet_wrap(facets = facet, scales = "free_x", nrow = nrow)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_sir
|
||||
#' @export
|
||||
scale_y_percent <- function(breaks = function(x) seq(0, max(x, na.rm = TRUE), 0.1), limits = NULL) {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(breaks, allow_class = c("numeric", "integer", "function"))
|
||||
meet_criteria(limits, allow_class = c("numeric", "integer"), has_length = 2, allow_NULL = TRUE, allow_NA = TRUE)
|
||||
|
||||
if (!is.function(breaks) && all(breaks[breaks != 0] > 1)) {
|
||||
breaks <- breaks / 100
|
||||
}
|
||||
ggplot2::scale_y_continuous(
|
||||
breaks = breaks,
|
||||
labels = if (is.function(breaks)) function(x) percentage(breaks(x)) else percentage(breaks),
|
||||
limits = limits
|
||||
)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_sir
|
||||
#' @export
|
||||
scale_sir_colours <- function(...,
|
||||
aesthetics = "fill") {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(aesthetics, allow_class = "character", is_in = c("alpha", "colour", "color", "fill", "linetype", "shape", "size"))
|
||||
# behaviour until AMR pkg v1.5.0 and also when coming from ggplot_sir()
|
||||
if ("colours" %in% names(list(...))) {
|
||||
original_cols <- c(
|
||||
S = "#3CAEA3",
|
||||
SI = "#3CAEA3",
|
||||
I = "#F6D55C",
|
||||
IR = "#ED553B",
|
||||
R = "#ED553B"
|
||||
)
|
||||
colours <- replace(original_cols, names(list(...)$colours), list(...)$colours)
|
||||
# limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
|
||||
# https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
|
||||
return(ggplot2::scale_fill_manual(values = colours, limits = force))
|
||||
}
|
||||
if (identical(unlist(list(...)), FALSE)) {
|
||||
return(invisible())
|
||||
}
|
||||
|
||||
names_susceptible <- c(
|
||||
"S", "SI", "IS", "S+I", "I+S", "susceptible", "Susceptible",
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible"),
|
||||
"replacement",
|
||||
drop = TRUE
|
||||
])
|
||||
)
|
||||
names_incr_exposure <- c(
|
||||
"I", "intermediate", "increased exposure", "incr. exposure",
|
||||
"Increased exposure", "Incr. exposure", "Susceptible, incr. exp.",
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Intermediate"),
|
||||
"replacement",
|
||||
drop = TRUE
|
||||
]),
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Susceptible, incr. exp."),
|
||||
"replacement",
|
||||
drop = TRUE
|
||||
])
|
||||
)
|
||||
names_resistant <- c(
|
||||
"R", "IR", "RI", "R+I", "I+R", "resistant", "Resistant",
|
||||
unique(TRANSLATIONS[which(TRANSLATIONS$pattern == "Resistant"),
|
||||
"replacement",
|
||||
drop = TRUE
|
||||
])
|
||||
)
|
||||
|
||||
susceptible <- rep("#3CAEA3", length(names_susceptible))
|
||||
names(susceptible) <- names_susceptible
|
||||
incr_exposure <- rep("#F6D55C", length(names_incr_exposure))
|
||||
names(incr_exposure) <- names_incr_exposure
|
||||
resistant <- rep("#ED553B", length(names_resistant))
|
||||
names(resistant) <- names_resistant
|
||||
|
||||
original_cols <- c(susceptible, incr_exposure, resistant)
|
||||
dots <- c(...)
|
||||
# replace S, I, R as colours: scale_sir_colours(mydatavalue = "S")
|
||||
dots[dots == "S"] <- "#3CAEA3"
|
||||
dots[dots == "I"] <- "#F6D55C"
|
||||
dots[dots == "R"] <- "#ED553B"
|
||||
cols <- replace(original_cols, names(dots), dots)
|
||||
# limits = force is needed in ggplot2 3.3.4 and 3.3.5, see here;
|
||||
# https://github.com/tidyverse/ggplot2/issues/4511#issuecomment-866185530
|
||||
ggplot2::scale_discrete_manual(aesthetics = aesthetics, values = cols, limits = force)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_sir
|
||||
#' @export
|
||||
theme_sir <- function() {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
ggplot2::theme_minimal(base_size = 10) +
|
||||
ggplot2::theme(
|
||||
panel.grid.major.x = ggplot2::element_blank(),
|
||||
panel.grid.minor = ggplot2::element_blank(),
|
||||
panel.grid.major.y = ggplot2::element_line(colour = "grey75"),
|
||||
# center title and subtitle
|
||||
plot.title = ggplot2::element_text(hjust = 0.5),
|
||||
plot.subtitle = ggplot2::element_text(hjust = 0.5)
|
||||
)
|
||||
}
|
||||
|
||||
#' @rdname ggplot_sir
|
||||
#' @export
|
||||
labels_sir_count <- function(position = NULL,
|
||||
x = "antibiotic",
|
||||
translate_ab = "name",
|
||||
minimum = 30,
|
||||
language = get_AMR_locale(),
|
||||
combine_SI = TRUE,
|
||||
datalabels.size = 3,
|
||||
datalabels.colour = "grey15") {
|
||||
stop_ifnot_installed("ggplot2")
|
||||
meet_criteria(position, allow_class = "character", has_length = 1, is_in = c("fill", "stack", "dodge"), allow_NULL = TRUE)
|
||||
meet_criteria(x, allow_class = "character", has_length = 1)
|
||||
meet_criteria(translate_ab, allow_class = c("character", "logical"), has_length = 1, allow_NA = TRUE)
|
||||
meet_criteria(minimum, allow_class = c("numeric", "integer"), has_length = 1, is_positive_or_zero = TRUE, is_finite = TRUE)
|
||||
language <- validate_language(language)
|
||||
meet_criteria(combine_SI, allow_class = "logical", has_length = 1)
|
||||
meet_criteria(datalabels.size, allow_class = c("numeric", "integer"), has_length = 1, is_positive = TRUE, is_finite = TRUE)
|
||||
meet_criteria(datalabels.colour, allow_class = "character", has_length = 1)
|
||||
|
||||
if (is.null(position)) {
|
||||
position <- "fill"
|
||||
}
|
||||
if (identical(position, "fill")) {
|
||||
position <- ggplot2::position_fill(vjust = 0.5, reverse = TRUE)
|
||||
}
|
||||
x_name <- x
|
||||
ggplot2::geom_text(
|
||||
mapping = ggplot2::aes_string(
|
||||
label = "lbl",
|
||||
x = x,
|
||||
y = "value"
|
||||
),
|
||||
position = position,
|
||||
inherit.aes = FALSE,
|
||||
size = datalabels.size,
|
||||
colour = datalabels.colour,
|
||||
lineheight = 0.75,
|
||||
data = function(x) {
|
||||
transformed <- sir_df(
|
||||
data = x,
|
||||
translate_ab = translate_ab,
|
||||
combine_SI = combine_SI,
|
||||
minimum = minimum,
|
||||
language = language
|
||||
)
|
||||
transformed$gr <- transformed[, x_name, drop = TRUE]
|
||||
transformed %pm>%
|
||||
pm_group_by(gr) %pm>%
|
||||
pm_mutate(lbl = paste0("n=", isolates)) %pm>%
|
||||
pm_ungroup() %pm>%
|
||||
pm_select(-gr)
|
||||
}
|
||||
)
|
||||
}
|
||||
|
||||
Reference in New Issue
Block a user