EpiMix_PlotSurvival: EpiMix_PlotSurvival function

In gevaertlab/EpiMix: EpiMix: an integrative tool for the population-level analysis of DNA methylation

EpiMix_PlotSurvival function

Description

function to plot Kaplan-meier survival curves for patients with different methylation state of a specific probe.

Usage

EpiMix_PlotSurvival(
  EpiMixResults,
  plot.probe,
  TCGA_CancerSite = NULL,
  clinical.df = NULL,
  font.legend = 16,
  font.x = 16,
  font.y = 16,
  font.tickslab = 14,
  legend = c(0.8, 0.9),
  show.p.value = TRUE
)

Arguments

EpiMixResults	List of objects returned from the EpiMix function
plot.probe	Character string with the name of the probe
TCGA_CancerSite	TCGA cancer code (e.g. 'LUAD')
clinical.df	(If the TCGA_CancerSite parameter has been specified, this parameter is optional) Dataframe with survival information. Must contain at least three columns: 'sample.id', 'days_to_death', 'days_to_last_follow_up'.
font.legend	numeric value indicating the font size of the figure legend. Default: 16
font.x	numeric value indicating the font size of the x axis label. Default: 16
font.y	numeric value indicating the font size of the y axis label. Default: 16
font.tickslab	numeric value indicating the font size of the axis tick label. Default: 14
legend	numeric vector indicating the x,y coordinate for positioning the figure legend. c(0,0) indicates bottom left, while c(1,1) indicates top right. Default: c(0.8,0.9). If 'none', legend will be removed.
show.p.value	logic indicating whether to show p value in the plot. P value was calculated by log-rank test. Default: TRUE.

Value

Kaplan-meier survival curve showing the survival time for patients with different methylation states of the probe.

Examples

library(survival)
library(survminer)

data(Sample_EpiMixResults_miRNA)

EpiMix_PlotSurvival(EpiMixResults = Sample_EpiMixResults_miRNA,
                    plot.probe = 'cg00909706',
                    TCGA_CancerSite = 'LUAD')

gevaertlab/EpiMix documentation built on July 20, 2023, 9:28 a.m.