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Plot Survival Tables

Source: R/ggsurvtable.R
ggsurvtable.Rd

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

Alboukadel Kassambara, alboukadel.kassambara@gmail.com

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