ggcoxzph: Graphical Test of Proportional Hazards with ggplot2

In survminer: Drawing Survival Curves using 'ggplot2'

Graphical Test of Proportional Hazards with ggplot2

Description

Displays a graph of the scaled Schoenfeld residuals, along with a smooth curve using ggplot2. Wrapper around plot.cox.zph.

Usage

ggcoxzph(
  fit,
  resid = TRUE,
  se = TRUE,
  df = 4,
  nsmo = 40,
  var,
  point.col = "red",
  point.size = 1,
  point.shape = 19,
  point.alpha = 1,
  caption = NULL,
  ggtheme = theme_survminer(),
  ...
)

## S3 method for class 'ggcoxzph'
print(x, ..., newpage = TRUE)

Arguments

fit	an object of class cox.zph.
resid	a logical value, if TRUE the residuals are included on the plot, as well as the smooth fit.
se	a logical value, if TRUE, confidence bands at two standard errors will be added.
df	the degrees of freedom for the fitted natural spline, df=2 leads to a linear fit.
nsmo	number of points used to plot the fitted spline.
var	the set of variables for which plots are desired. By default, plots are produced in turn for each variable of a model.
point.col, point.size, point.shape, point.alpha	color, size, shape and visibility to be used for points.
caption	the caption of the final grob (bottom in arrangeGrob)
ggtheme	function, ggplot2 theme name. Allowed values include ggplot2 official themes: see theme.
...	further arguments passed to either the print() function or to the ggpar function for customizing the plot (see Details section).
x	an object of class ggcoxzph
newpage	open a new page. See grid.arrange.

Details

Customizing the plots: The plot can be easily customized using additional arguments to be passed to the function ggpar(). Read ?ggpubr::ggpar. These arguments include font.main,font.submain,font.caption,font.x,font.y,font.tickslab,font.legend: a vector of length 3 indicating respectively the size (e.g.: 14), the style (e.g.: "plain", "bold", "italic", "bold.italic") and the color (e.g.: "red") of main title, subtitle, caption, xlab and ylab and axis tick labels, respectively. For example font.x = c(14, "bold", "red"). Use font.x = 14, to change only font size; or use font.x = "bold", to change only font face.

Value

Returns an object of class ggcoxzph which is a list of ggplots.

Functions

• ggcoxzph(): Graphical Test of Proportional Hazards using ggplot2.

Author(s)

Marcin Kosinski , [e-mail]

Examples

library(survival)
fit <- coxph(Surv(futime, fustat) ~ age + ecog.ps + rx, data=ovarian)
cox.zph.fit <- cox.zph(fit)
# plot all variables
ggcoxzph(cox.zph.fit)
# plot all variables in specified order
ggcoxzph(cox.zph.fit, var = c("ecog.ps", "rx", "age"), font.main = 12)
# plot specified variables in specified order
ggcoxzph(cox.zph.fit, var = c("ecog.ps", "rx"), font.main = 12, caption = "Caption goes here")

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