https://github.com/cran/cutpointr
Tip revision: 7e56c827a694247d212e9a0167a119f917e1f31b authored by Christian Thiele on 31 August 2018, 15:50:10 UTC
version 0.7.4
version 0.7.4
Tip revision: 7e56c82
plot_sensitivity_specificity.R
#' Sensitivity and specificity plot from a cutpointr object
#'
#' Given a \code{cutpointr} object this function plots the sensitivity and specificity
#' curve(s) per subgroup, if the latter is given.
#' @param x A cutpointr object.
#' @param display_cutpoint (logical) Whether or not to display the optimal
#' cutpoint as a dot on the precision recall curve.
#' @param ... Additional arguments (unused).
#' @examples
#' library(cutpointr)
#'
#' ## Optimal cutpoint for dsi
#' data(suicide)
#' opt_cut <- cutpointr(suicide, dsi, suicide)
#' plot_sensitivity_specificity(opt_cut)
#' @family cutpointr plotting functions
#' @export
#' @importFrom purrr %>%
plot_sensitivity_specificity <- function(x, display_cutpoint = TRUE, ...) {
stopifnot("cutpointr" %in% class(x))
args <- list(...)
if (!(has_column(x, "subgroup"))) {
dts_pr <- c("roc_curve", "optimal_cutpoint")
ltype <- NULL
} else {
dts_pr <- c("roc_curve", "subgroup", "optimal_cutpoint")
ltype <- ~ subgroup
}
if (!(has_column(x, "subgroup"))) {
plot_title <- ggplot2::ggtitle("Sensitivity and specificity plot")
} else {
plot_title <- ggplot2::ggtitle("Sensitivity and specificity plot",
"by class")
}
for (r in 1:nrow(x)) {
x$roc_curve[[r]] <- x$roc_curve[[r]] %>%
dplyr::mutate_(Sensitivity = ~ tp / (tp + fn),
Specificity = ~ tn / (tn + fp))
}
res_unnested <- x %>%
dplyr::select_(.dots = dts_pr) %>%
tidyr::unnest_(unnest_cols = c("roc_curve"))
res_unnested <- x %>%
tidyr::unnest_(unnest_cols = c("roc_curve"))
res_unnested <- res_unnested[is.finite(res_unnested$x.sorted), ]
res_unnested <- tidyr::gather_(res_unnested, key_col = "metric",
value_col = "value",
gather_cols = c("Sensitivity", "Specificity"))
pr <- ggplot2::ggplot(res_unnested,
ggplot2::aes_(x = ~ x.sorted, y = ~ value,
color = ~ metric, linetype = ltype)) +
ggplot2::geom_line() +
plot_title +
ggplot2::xlab("Cutpoint") +
ggplot2::ylab("Sensitivity and Specificity")
if (display_cutpoint) {
if (!(has_column(x, "subgroup"))) {
res_cutpoints <- x %>%
dplyr::select_(.dots = "optimal_cutpoint")
if (is.list(res_cutpoints$optimal_cutpoint)) {
res_cutpoints <- tidyr::unnest_(res_cutpoints)
}
} else {
res_cutpoints <- x %>%
dplyr::select_(.dots = list("optimal_cutpoint", "subgroup"))
if (is.list(res_cutpoints$optimal_cutpoint)) {
res_cutpoints <- tidyr::unnest_(res_cutpoints)
}
}
pr <- pr +
ggplot2::geom_vline(data = res_cutpoints,
ggplot2::aes_(xintercept = ~ optimal_cutpoint,
linetype = ltype))
}
return(pr)
}