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

Description Usage Arguments Value See Also Examples

Description

Plot results from Cox regression analysis for dual regulons

Usage

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## 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

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# 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")

RTNsurvival documentation built on Nov. 12, 2020, 2 a.m.