geom_rocci: Confidence regions for the ROC curve

Description

Display rectangular confidence regions for the empirical ROC curve.

Usage

geom_rocci(
  mapping = NULL,
  data = NULL,
  stat = "rocci",
  ci.at = NULL,
  sig.level = 0.05,
  na.rm = TRUE,
  alpha.box = 0.3,
  labels = TRUE,
  labelsize = 3.88,
  labelround = 1,
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  ...
)
GeomRocci

Format

An object of class GeomRocci (inherits from Geom, ggproto, gg) of length 6.

Arguments

mapping

Set of aesthetic mappings created by aes() or aes_(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

Use to override the default connection between geom_rocci and stat_rocci.

ci.at

Vector of values in the range of the biomarker where confidence regions will be displayed

sig.level

Significance level for the confidence regions

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

alpha.box

Alpha level for the confidence regions

labels

If TRUE, adds text labels for the cutoffs where the confidence regions are displayed

labelsize

Size of cutoff text labels

labelround

Integer, number of significant digits to round cutoff labels

position

Position adjustment, either as a string, or the result of a call to a position adjustment function.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

...

Other arguments passed on to layer(). These are often aesthetics, used to set an aesthetic to a fixed value, like colour = "red" or size = 3. They may also be parameters to the paired geom/stat.

Aesthetics

geom_rocci understands the following aesthetics (required aesthetics are in bold). stat_rocci automatically maps the estimates to the required aesthetics:

x The FPF estimate
y The TPF estimate
xmin Lower confidence limit for the FPF
xmax Upper confidence limit for the FPF
ymin Lower confidence limit for the TPF
ymax Upper confidence limit for the TPF
alpha
color
fill
linetype
size

Examples

Run this code


D.ex <- rbinom(50, 1, .5)
rocdata <- data.frame(D = c(D.ex, D.ex), 
                   M = c(rnorm(50, mean = D.ex, sd = .4), rnorm(50, mean = D.ex, sd = 1)), 
                   Z = c(rep("A", 50), rep("B", 50)))

ggplot(rocdata, aes(m = M, d = D)) + geom_roc() + geom_rocci()
ggplot(rocdata, aes(m = M, d = D, color = Z)) + geom_roc() + geom_rocci()
ggplot(rocdata, aes(m = M, d = D, color = Z)) + geom_roc() + geom_rocci(sig.level = .01)
ggplot(rocdata, aes(m = M, d = D)) + geom_roc(n.cuts = 0) + 
geom_rocci(ci.at = quantile(rocdata$M, c(.1, .25, .5, .75, .9)))
ggplot(rocdata, aes(m = M, d = D, color = Z)) + geom_roc() + geom_rocci(linetype = 1)