R: Graphical Test of Proportional Hazards with ggplot2

ggcoxzph {survminer} | R Documentation

## 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 , m.p.kosinski@gmail.com

### 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")

[Package survminer version 0.4.1 Index]