vr_plot: Create a 'ggplot' directly from an object through an S3...

In visR-sandbox/visR-survival: A package to wrap functionality for plots, tables and diagrams adhering to graphical principles

Description

S3 method for creating plots directly from objects using 'ggplot2', similar to base plot function. The default method is base::plot.

Usage

vr_plot(x, ...)

## Default S3 method:
vr_plot(x, ...)

## S3 method for class 'survfit'
vr_plot(
  survfit_object = NULL,
  y_label = NULL,
  x_label = NULL,
  x_units = NULL,
  x_ticks = NULL,
  y_ticks = NULL,
  fun = "surv",
  legend_position = "right"
)

Arguments

x	object to be passed on to the method
...	other arguments passed on to the method
survfit_object	Object of class 'survfit'
y_label	character Label for the y-axis. When not specified, the default will do a proposal, depending on the 'fun' argument.
x_label	character Label for the x-asis. When not specified, the algorithm will look for "PARAM" information inside the list structure of the 'survfit' object. Note that this information is automatically added when using visR::vr_KM_est and when the input data has the variable "PARAM". If no "PARAM" information is available "time" is used as label.
x_ticks	Ticks for the x-axis. When not specified, the default will do a proposal.
y_ticks	Ticks for the y-axis. When not specified, the default will do a proposal based on the 'fun' argument.
fun	Arbitrary function defining a transformation of the survival curve. This argument will also influence the y_ticks and y_label if not specified. "surv": survival curve on the probability scale. The default y label will state "Survival probability". "log": log survival curve. The default y label will state "log(Survival probability)". "event": empirical CDF f(y) = 1-y. The default y label will state "Failure probability". "cloglog": complimentary log-log survival f(y) = log(-log(y)). The default y label will state "log(-log(Survival probability))". "pct": survival curve, expressed as percentage. The default y label will state "Survival probability (%)". "logpct": log survival curve, expressed as percentage. The default y label will state "log(Survival probability (%))". "cumhaz": MLE estimate of the cumulative hazard f(y) = -log(y). The default y label will state "cumulative hazard".
legend_position	Specifies the legend position in the plot. Character values allowed are "top" "left" "bottom" "right". Numeric coordinates are also allowed. Default is "right".
x_unit	Unit to be added to the x_label (x_label (x_unit)). Default is NULL.

Value

Object of class ggplot ggsurvplot.

Author(s)

Steven Haesendonckx

See Also

ggplot

Examples

library(survival)
library(dplyr)
library(tidyr)
library(ggplot2)

survfit_object <- vr_KM_est(data = adtte, strata = "TRTP")

## Plot survival probability
vr_plot(survfit_object = survfit_object, fun = "surv")
vr_plot(survfit_object, fun = "pct")

## Plot cumulative hazard
vr_plot(survfit_object, fun = "cloglog")
 

visR-sandbox/visR-survival documentation built on Sept. 18, 2020, 6:21 p.m.