tnsPlotKmInteraction-methods: Plot results from Kaplan-Meier analysis for dual regulons

In csgroen/RTNsurvival: Survival analysis using transcriptional networks inferred by the RTN package

Description

Plot results from Kaplan-Meier analysis for dual regulons

Usage

## S4 method for signature 'TNS'
tnsPlotKmInteraction(tns, dualreg = NULL,
  fname = "kmInteraction", fpath = ".", xlab = "Months",
  ylab = "Survival probability", colorPalette = "bluered", width = 4,
  height = 4, plotpdf = FALSE)

Arguments

tns	A TNS object, which must have passed GSEA2 analysis.
dualreg	A character string with the name of a dual regulon.
fname	A string. The name of the file in which the plot will be saved
fpath	A string. The path to the directory where the plot will be saved
xlab	A string. The label for the x axis on the third panel. This should be the measure of time shown in the survival data.frame after the last check-up.
ylab	A string. The label for the y axis on the third panel
colorPalette	A string, which can be 'red', 'blue', 'redblue', or 'bluered'. Alternatively, it can be a vector of five colors or hex values.
width	A numeric value. Represents the width of the plot.
height	A numeric value. Represents the height of the plot.
plotpdf	A logical value. If TRUE, the plot is saved as a pdf file. If false, it is plotted in the plotting area.

Value

A plot, showing a graphical analysis for the 'tnsKmInteraction' function.

Examples

# load survival data
data(survival.data)

# load TNI-object
data(stni, package = "RTN")

stns <- tni2tnsPreprocess(stni, survivalData = survival.data, 
keycovar = c('Grade','Age'), time = 1, event = 2)
stns <- tnsGSEA2(stns)

# KM analysis for dual regulons
# stns <- tnsKmInteraction(stns, stepFilter=FALSE)
# tnsPlotKmInteraction(stns, dualreg = "FOXM1~PTTG1")

csgroen/RTNsurvival documentation built on May 20, 2019, 1:49 p.m.