survminer (version 0.2.4)

ggcoxdiagnostics: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2

Description

Displays diagnostics graphs presenting goodness of Cox Proportional Hazards Model fit, that can be calculated with coxph function.

Usage

ggcoxdiagnostics(fit, type = c("martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas", "scaledsch", "partial"), ..., linear.predictions = TRUE, hline = TRUE, hline.col = "red", hline.size = 1, hline.alpha = 1, hline.yintercept = 0, hline.lty = "dashed", point.col = "black", point.size = 1, point.shape = 19, point.alpha = 1, font.main = c(16, "plain", "black"), font.x = c(14, "plain", "black"), font.y = c(14, "plain", "black"), font.tickslab = c(12, "plain", "black"), ggtheme = ggplot2::theme_bw())

Arguments

fit

an object of class coxph.object - created with coxph function.

type

the type of residuals to present on Y axis of a diagnostic plot. The same as in residuals.coxph: character string indicating the type of residual desired. Possible values are "martingale", "deviance", "score", "schoenfeld", "dfbeta", "dfbetas" and "scaledsch". Only enough of the string to determine a unique match is required.

...

furthere arguments passed to residuals.coxph.

linear.predictions

a logical value indicating whether to show linear predictions for observations (TRUE) or just indexed of observations (FALSE) on X axis.

hline

a logical - should the horizontal line be added to highlight the Y=0 level.

hline.col, hline.size, hline.lty, hline.alpha, hline.yintercept

color, size, linetype, visibility and Y-axis coordinate to be used for geom_hline. Used only when hline = TRUE.

point.col, point.size, point.shape, point.alpha

color, size, shape and visibility to be used for points.

font.main, font.x, font.y, font.tickslab

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, 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.

ggtheme

function, ggplot2 theme name. Default value is ggplot2::theme_bw(). Allowed values include ggplot2 official themes: see theme.

Value

Returns an object of class ggplot.

Functions

• ggcoxdiagnostics: Diagnostic Plots for Cox Proportional Hazards Model with ggplot2

Examples

if(require(RTCGA.clinical)){
# TCGA data exmaple (http://cancergenome.nih.gov/)
# source("https://bioconductor.org/biocLite.R")
# biocLite("RTCGA.clinical") # data for examples
# library(RTCGA.clinical) # also loads 'RTCGA' package
survivalTCGA(BRCA.clinical, OV.clinical,
            extract.cols = c("admin.disease_code", "patient.days_to_birth")) -> BRCAOV.survInfo
BRCAOV.survInfo$age  <- round((-as.numeric(BRCAOV.survInfo$patient.days_to_birth))/365,2)

library(survival)
coxph.fit <- coxph(Surv(times, patient.vital_status) ~ admin.disease_code + age,
              data = BRCAOV.survInfo)

ggcoxdiagnostics(coxph.fit, ggtheme = theme_dark(), point.col = "white", point.aplha = 0.3)
ggcoxdiagnostics(coxph.fit, ggtheme = theme_RTCGA(), # library(RTCGA.clinical)
 type = "deviance") + ylab('Deviance Residuals')
ggcoxdiagnostics(coxph.fit, ggtheme = theme_light(), linear.predictions = FALSE)
# ggcoxdiagnostics(coxph.fit, ggtheme = theme_void(), type = "deviance", linear.predictions = FALSE)
}

# traditional example
library(survival)
coxph.fit2 <- coxph(Surv(futime, fustat) ~ age + ecog.ps, data=ovarian)
ggcoxdiagnostics(coxph.fit2, type = "deviance")