R: Add tick marks to a Kaplan-Meier survival curve

geom_kmticks {ggquickeda}

R Documentation

Add tick marks to a Kaplan-Meier survival curve

Description

Adds tickmarks at the times when there are censored observations but no events

Usage

geom_kmticks(
  mapping = NULL,
  data = NULL,
  stat = "kmticks",
  position = "identity",
  show.legend = NA,
  inherit.aes = TRUE,
  na.rm = TRUE,
  ...
)

Arguments

`mapping`	Set of aesthetic mappings created by `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`	The statistical transformation to use on the data for this layer, either as a `ggproto` `Geom` subclass or as a string naming the stat stripped of the `stat_` prefix (e.g. `"count"` rather than `"stat_count"`)
`position`	Position adjustment, either as a string naming the adjustment (e.g. `"jitter"` to use `position_jitter`), or the result of a call to a position adjustment function. Use the latter if you need to change the settings of the adjustment.
`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()`.
`na.rm`	If `FALSE`, the default, missing values are removed with a warning. If `TRUE`, missing values are silently removed.
`...`	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_kmticks understands the following aesthetics (required aesthetics are in bold):

x The survival/censoring times. This is automatically mapped by stat_kmticks()
y The survival probability estimates. This is automatically mapped by stat_kmticks() smallest level in sort order is assumed to be 0, with a warning
alpha
color
linetype
size

Examples

library(ggplot2)
sex <- rbinom(250, 1, .5)
df <- data.frame(time = exp(rnorm(250, mean = sex)), status = rbinom(250, 1, .75), sex = sex)
ggplot(df, aes(time = time, status = status, color = factor(sex), group = factor(sex))) +
 geom_km() + geom_kmticks(col="black")