survivalAnalysis (version 0.4.0)

kaplan_meier_plot: Kaplan Meier plots from survival results.

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)

Value

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

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. If you want to combine two curves in one plot (ggsurvplot_combine), wrap them in in_one_kaplan_meier_plot when passing as argument here. (otherwise you will get a list with separate plots for each) 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

• ggplot.add: ggplot2 object to add to the ggplot plot part of the created KM plot. One common use case is manual specification of the line type, which is currently not possible with ggsurvplot. The passed object can be result of "+" operations will be added via "+" as usual with ggplot() objects.

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".

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))