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(v2.1.1.9188) fix antibiogram plot

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dr. M.S. (Matthijs) Berends
2025-03-07 23:01:25 +01:00
parent b67613ce08
commit 245483e41c
10 changed files with 39 additions and 19 deletions
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46
R/antibiogram.R
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@ -769,6 +769,32 @@ antibiogram.default <- function(x,
# prepare for definitive output
out <- out_wisca
wisca_parameters <- wisca_parameters[, colnames(wisca_parameters)[!colnames(wisca_parameters) %in% c(levels(NA_sir_), "lower_ci", "upper_ci", "group")], drop = FALSE]
if (isTRUE(has_syndromic_group)) {
long_numeric <- out_wisca %pm>%
pm_ungroup() %pm>%
pm_select(
syndromic_group = syndromic_group,
ab = ab,
coverage = coverage,
lower_ci = lower_ci,
upper_ci = upper_ci,
n_total = n_total,
n_tested = n_tested,
n_susceptible = n_susceptible
)
} else {
long_numeric <- out_wisca %pm>%
pm_ungroup() %pm>%
pm_select(
ab = ab,
coverage = coverage,
lower_ci = lower_ci,
upper_ci = upper_ci,
n_total = n_total,
n_tested = n_tested,
n_susceptible = n_susceptible
)
}
}
out$digits <- digits # since pm_sumarise() cannot work with an object outside the current frame
@ -1170,9 +1196,7 @@ tbl_format_footer.antibiogram <- function(x, ...) {
plot.antibiogram <- function(x, ...) {
df <- attributes(x)$long_numeric
if (!"mo" %in% colnames(df)) {
stop_("Plotting antibiograms using `plot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.",
call = FALSE
)
df$mo <- ""
}
if ("syndromic_group" %in% colnames(df)) {
# barplot in base R does not support facets - paste columns together
@ -1226,9 +1250,7 @@ barplot.antibiogram <- function(height, ...) {
autoplot.antibiogram <- function(object, ...) {
df <- attributes(object)$long_numeric
if (!"mo" %in% colnames(df)) {
stop_("Plotting antibiograms using `autoplot()` is only possible if they were not created using dplyr groups. See `?antibiogram` for how to retrieve numeric values in a long format for advanced plotting.",
call = FALSE
)
df$mo <- ""
}
out <- ggplot2::ggplot(df,
mapping = ggplot2::aes(
@ -1243,6 +1265,10 @@ autoplot.antibiogram <- function(object, ...) {
) +
ggplot2::geom_col(position = ggplot2::position_dodge2(preserve = "single")) +
ggplot2::facet_wrap("mo") +
ggplot2::geom_errorbar(
mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
position = ggplot2::position_dodge2(preserve = "single", width = 1)
) +
ggplot2::labs(
y = ifelse(isTRUE(attributes(object)$combine_SI), "%SI", "%S"),
x = NULL,
@ -1252,14 +1278,6 @@ autoplot.antibiogram <- function(object, ...) {
NULL
}
)
if (isTRUE(attributes(object)$wisca)) {
out <- out +
ggplot2::geom_errorbar(
mapping = ggplot2::aes(ymin = lower_ci * 100, ymax = upper_ci * 100),
position = ggplot2::position_dodge2(preserve = "single"),
width = 0.5
)
}
out
}