plotPathwayKM: Plot KM of the pathway by omics

Description Usage Arguments

Description

Given the pathway, it creates the Kaplan-meier curves following the formula.

Usage

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plotPathwayKM(pathway, formula = "Surv(days, status) ~ PC1",
  fileName = NULL, paletteNames = NULL, h = 9, w = 7,
  risk.table = TRUE, pval = TRUE, size = 1, inYears = FALSE,
  discr_prop_pca = 0.15, discr_prop_events = 0.05,
  additional_discrete = NULL, additional_continous = NULL)

Arguments

pathway

MultiOmicsModule pathway object

formula

a formula to compute the plot

fileName

optional filenames to save the plot

paletteNames

three palettes

h

the height of the plot

w

the width of the plot

risk.table

logical to show risk.table

pval

logical to show pvalue

size

line width of the KM curves

inYears

set time in years

discr_prop_pca

the minimal proportion to compute the pca classes

discr_prop_events

the minimal proportion to compute the event classes

additional_discrete

names of the additional discrete variables to include

additional_continous

names of the additional continous variables to include


cavei/MOSClip documentation built on May 12, 2019, 5:22 p.m.