tnsPlotCoxInteraction-methods: Plot results from Cox regression analysis for dual regulons

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

Description

Plot results from Cox regression analysis for dual regulons

Usage

## S4 method for signature 'TNS'
tnsPlotCoxInteraction(tns, dualreg, xlim = NULL,
  ylim = NULL, hlim = NULL, hcols = c("#008080ff", "#d45500ff"),
  showdata = TRUE, colorPalette = "bluered",
  fname = "coxInteraction", fpath = ".", width = 4.5, height = 4,
  plotype = "3D", plotpdf = FALSE)

Arguments

tns	A 'TNS' object with regulons used to compute the dual regulon.
dualreg	A character string with the name of a dual regulon.
xlim	A numeric vector of length 2, i.e. xlim = c(x1, x2), indicating the limits of the plot for the first member of the dual regulon. If xlim = NULL, it will be derevided from the observed data ranges. Values must be in the range [-2,2].
ylim	A numeric vector of length 2, i.e. ylim = c(y1, y2), indicating the limits of the plot for the second member of the dual regulon. If ylim = NULL, it will be derevided from the observed data ranges. Values must be in the range [-2,2]. If plotype='2D', ylim represents the two fixed values for the second member of the dual regulon.
hlim	A numeric vector of length 2, i.e. hlim = c(h1, h2), indicating the limits of the plot for the Hazard Ratio (HR). If hlim = NULL, it will be derevided from the observed data ranges. If plotype='2D', HR is represented in the y-axis.
hcols	A vector of length 2 indicating a diverging color scheme for the Hazard Ratio (HR).
showdata	A logical value indicating whether to show the original data used to fit linear model.
colorPalette	A string, which can be 'red', 'blue', 'redblue', or 'bluered'. Alternatively, it can be a vector of five colors or hex values.
fname	A string. The name of the PDF file (when plotpdf=TRUE).
fpath	A string. The directory where the file will be saved.
width	A numeric value. The width of the plot.
height	A numeric value. The height of the plot.
plotype	A string indicating '2D' of '3D' plot type. If plotype = '2D', the Hazard Ratio is represented in the y-axis.
plotpdf	A logical value.

Value

A Cox hazard model plot and statistics.

A 3D heatmap plot.

See Also

tnsKM, tnsCox

Examples

# load survival data
data(survival.data)

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

# perform survival analysis for regulons
stns <- tni2tnsPreprocess(stni, survivalData = survival.data, time = 1, event = 2)
stns <- tnsGSEA2(stns, verbose=FALSE)

# run Cox regression for dual regulons
# stns <- tnsCoxInteraction(stns, stepFilter = FALSE)
# tnsPlotCoxInteraction(stns, dualreg = "FOXM1~PTTG1")

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