Skip to main content
  • Home
  • Development
  • Documentation
  • Donate
  • Operational login
  • Browse the archive

swh logo
SoftwareHeritage
Software
Heritage
Archive
Features
  • Search

  • Downloads

  • Save code now

  • Add forge now

  • Help

  • c49f88d
  • /
  • plot_sensitivity_specificity.R
Raw File Download

To reference or cite the objects present in the Software Heritage archive, permalinks based on SoftWare Hash IDentifiers (SWHIDs) must be used.
Select below a type of object currently browsed in order to display its associated SWHID and permalink.

  • content
  • directory
content badge
swh:1:cnt:873f2e9010be5c29311d0beb21e5507e7ba86dbe
directory badge
swh:1:dir:c49f88dc4461ee4f7d969eefddc5d36e2726b09d

This interface enables to generate software citations, provided that the root directory of browsed objects contains a citation.cff or codemeta.json file.
Select below a type of object currently browsed in order to generate citations for them.

  • content
  • directory
(requires biblatex-software package)
Generating citation ...
(requires biblatex-software package)
Generating citation ...
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"))
    # Drop possible NaN at x.sorted = Inf or -Inf
    res_unnested <- stats::na.omit(res_unnested)
    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)
}

back to top

Software Heritage — Copyright (C) 2015–2026, The Software Heritage developers. License: GNU AGPLv3+.
The source code of Software Heritage itself is available on our development forge.
The source code files archived by Software Heritage are available under their own copyright and licenses.
Terms of use: Archive access, API— Content policy— Contact— JavaScript license information— Web API