Graphical Test of Proportional Hazards with ggplot2
Displays a graph of the scaled Schoenfeld residuals, along with a smooth curve using ggplot2. Wrapper around plot.cox.zph.
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)
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 ( |
ggtheme |
function, ggplot2 theme name.
Allowed values include ggplot2 official themes: see |
... |
further arguments passed to either the print() function or to the |
x |
an object of class ggcoxzph |
newpage |
open a new page. See |
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.
Returns an object of class ggcoxzph which is a list of ggplots.
ggcoxzph: Graphical Test of Proportional Hazards using ggplot2.
Marcin Kosinski , m.p.kosinski@gmail.com
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")Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.