ggsurvtable: Plot Survival Tables

In survminer: Drawing Survival Curves using 'ggplot2'

Plot Survival Tables

Description

Plot survival tables:

• ggrisktable(): Plot the number at risk table.

• ggcumevents(): Plot the cumulative number of events table.

• ggcumcensor(): Plot the cumulative number of censored subjects, the number of subjects who exit the risk set, without an event, at time t. Normally, users don't need to use this function directly.

• ggsurvtable(): Generic function to plot any survival tables.

Normally, users don't need to use this function directly. Internally used by the function ggsurvplot.

Usage

ggrisktable(
  fit,
  data = NULL,
  risk.table.type = c("absolute", "percentage", "abs_pct", "nrisk_cumcensor",
    "nrisk_cumevents"),
  ...
)

ggcumevents(fit, data = NULL, ...)

ggcumcensor(fit, data = NULL, ...)

ggsurvtable(
  fit,
  data = NULL,
  survtable = c("cumevents", "cumcensor", "risk.table"),
  risk.table.type = c("absolute", "percentage", "abs_pct", "nrisk_cumcensor",
    "nrisk_cumevents"),
  title = NULL,
  risk.table.title = NULL,
  cumevents.title = title,
  cumcensor.title = title,
  color = "black",
  palette = NULL,
  break.time.by = NULL,
  xlim = NULL,
  xscale = 1,
  xlab = "Time",
  ylab = "Strata",
  xlog = FALSE,
  legend = "top",
  legend.title = "Strata",
  legend.labs = NULL,
  y.text = TRUE,
  y.text.col = TRUE,
  fontsize = 4.5,
  font.family = "",
  axes.offset = TRUE,
  ggtheme = theme_survminer(),
  tables.theme = ggtheme,
  ...
)

Arguments

fit	an object of class survfit. Can be a list containing two components: 1) time: time variable used in survfit; 2) table: survival table as generated by the internal function .get_timepoints_survsummary(). Can be also a simple data frame.
data	a dataset used to fit survival curves. If not supplied then data will be extracted from 'fit' object.
risk.table.type	risk table type. Allowed values include: "absolute" or "percentage": to show the absolute number and the percentage of subjects at risk by time, respectively. Use "abs_pct" to show both absolute number and percentage. Used only when survtable = "risk.table".
...	other arguments passed to the function ggsurvtable and ggpar.
survtable	a character string specifying the type of survival table to plot.
title	the title of the plot.
risk.table.title	The title to be used for the risk table.
cumevents.title	The title to be used for the cumulative events table.
cumcensor.title	The title to be used for the cumcensor table.
color	color to be used for the survival curves. If the number of strata/group (n.strata) = 1, the expected value is the color name. For example color = "blue". If n.strata > 1, the expected value is the grouping variable name. By default, survival curves are colored by strata using the argument color = "strata", but you can also color survival curves by any other grouping variables used to fit the survival curves. In this case, it's possible to specify a custom color palette by using the argument palette.
palette	the color palette to be used. Allowed values include "hue" for the default hue color scale; "grey" for grey color palettes; brewer palettes e.g. "RdBu", "Blues", ...; or custom color palette e.g. c("blue", "red"); and scientific journal palettes from ggsci R package, e.g.: "npg", "aaas", "lancet", "jco", "ucscgb", "uchicago", "simpsons" and "rickandmorty". See details section for more information. Can be also a numeric vector of length(groups); in this case a basic color palette is created using the function palette.
break.time.by	numeric value controlling time axis breaks. Default value is NULL.
xlim	x axis limits e.g. xlim = c(0, 1000).
xscale	numeric or character value specifying x-axis scale. If numeric, the value is used to divide the labels on the x axis. For example, a value of 365.25 will give labels in years instead of the original days. If character, allowed options include one of c("d_m", "d_y", "m_d", "m_y", "y_d", "y_m"), where d = days, m = months and y = years. For example, xscale = "d_m" will transform labels from days to months; xscale = "m_y", will transform labels from months to years.
xlab	x axis label
ylab	y axis label
xlog	logical value. If TRUE, x axis is tansformed into log scale.
legend	character specifying legend position. Allowed values are one of c("top", "bottom", "left", "right", "none"). Default is "top" side position. to remove the legend use legend = "none". Legend position can be also specified using a numeric vector c(x, y); see details section.
legend.title	legend title.
legend.labs	character vector specifying legend labels. Used to replace the names of the strata from the fit. Should be given in the same order as those strata.
y.text	logical. Default is TRUE. If FALSE, the table y axis tick labels will be hidden.
y.text.col	logical. Default value is FALSE. If TRUE, the table tick labels will be colored by strata.
fontsize	text font size.
font.family	character vector specifying text element font family, e.g.: font.family = "Courier New".
axes.offset	logical value. Default is TRUE. If FALSE, set the plot axes to start at the origin.
ggtheme	function, ggplot2 theme name. Default value is theme_survminer. Allowed values include ggplot2 official themes: see theme.
tables.theme	function, ggplot2 theme name. Default value is theme_survminer. Allowed values include ggplot2 official themes: see theme. Note that, tables.theme is incremental to ggtheme.

Value

a ggplot.

Functions

• ggrisktable(): Plot the number at risk table.

• ggcumevents(): Plot the cumulative number of events table

• ggcumcensor(): Plot the cumulative number of censor table

• ggsurvtable(): Generic function to plot survival tables: risk.table, cumevents and cumcensor

Author(s)

Alboukadel Kassambara, [e-mail]

Examples

# Fit survival curves
#:::::::::::::::::::::::::::::::::::::::::::::::
require("survival")
fit<- survfit(Surv(time, status) ~ sex, data = lung)

# Survival tables
#:::::::::::::::::::::::::::::::::::::::::::::::
tables <- ggsurvtable(fit, data = lung, color = "strata",
  y.text = FALSE)

# Risk table
tables$risk.table

# Number of cumulative events
tables$cumevents

# Number of cumulative censoring
tables$cumcensor

survminer documentation built on Oct. 30, 2024, 5:06 p.m.