kaplan_meier_plot: Kaplan Meier plots from survival results.

In survivalAnalysis: High-Level Interface for Survival Analysis and Associated Plots

Description

Uses ggsurvplot from the survminer package to create publication-ready plots.

Usage

kaplan_meier_plot(..., mapped_plot_args = list(), p_lessthan_cutoff = 0.001)

Arguments

...	One or many SurvivalAnalysisResult objects as returned by analyse_survival and arguments that will be passed to ggsurvplot. Bare lists will be spliced. If using lists, the same argument may be contained in multiple lists; in this case, the last occurrence is used, i.e. you can first pass a list with default arguments, and then override some of them. In addition to all arguments supported by ggsurvplot, these arguments and shortcuts can be used additionally: break.time.by: breakByYear, breakByHalfYear, breakByQuarterYear, breakByMonth (numeric value only in ggsurvplot) xscale: scaleByYear, scaleByMonth (numeric value only in ggsurvplot) hazard.ratio (logical): display hazard ratios in addition to p value, complementing pval=T xlab: {.OS,.PFS,.TTF,.DFS}.{years,months,days} table.layout: clean, displays risk table only with color code and number, no grid, axes or labels. (do not forget risk.table=TRUE to see something) papersize: numeric vector of length 2, c(width, height), unit inches. kaplan_meier_plot will store a "papersize" attribute with this value which is read by save_pdf
mapped_plot_args	Optionally, if given n objects to plot, a named list of vectors of size n. The name is an argument names passed to ggsurvplot. The elements of the vector will be mapped 1:1 to each object. This allows to perform batch plotting where only few arguments differ (e.g. titles A, B, C...) between the plots.
p_lessthan_cutoff	The lower limit below which p value will be displayed as "less than". If p_lessthan_cutoff == 0.001, the a p value of 0.002 will be displayed as is, while 0.0005 will become "p < 0.001".

Value

If given one result to plot, one ggsurvplot object; if given more than one result, a list of ggsurvplot objects.

Examples

library(magrittr)
library(dplyr)
survival::aml %>%
  analyse_survival(vars(time, status), x) %>%
  kaplan_meier_plot(break.time.by="breakByMonth",
                    xlab=".OS.months",
                    risk.table=TRUE,
                    ggtheme=ggplot2::theme_bw(10))

Example output

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Warning message:
Vectorized input to `element_text()` is not officially supported.
Results may be unexpected or may change in future versions of ggplot2. 

survivalAnalysis documentation built on April 24, 2021, 5:07 p.m.