tnsPlotCox,TNS-method {RTNsurvival} | R Documentation

## Cox plots for TNS class objects

### Description

Run Cox multivariate regression for regulons and key covariables.

### Usage

    ## S4 method for signature 'TNS'
    tnsPlotCox(
      tns,
      regs = NULL,
      fname = "coxplot",
      fpath = ".",
      ylab = "Regulons and other covariates",
      xlab = "Hazard Ratio (95% CI)",
      width = 5,
      height = 5,
      xlim = c(0.3, 3),
      sortregs = TRUE,
      plotpdf = FALSE
    )

### Arguments

`tns` | A TNS object, which must have passed GSEA2 analysis.
`regs` | An optional string vector specifying regulons to make the plot.
`fname` | A string. The name of the PDF file which will contain the plot.
`fpath` | A string. The directory where the file will be saved.
`ylab` | A string. The label of the y-axis, describing what is represented.
`xlab` | A string. The label of the x-axis.
`width` | A numeric value. The width of the plot.
`height` | A numeric value. The height of the plot.
`xlim` | A vector with 2 values indicating lowest and highest HR values.
`sortregs` | A logical value. If TRUE, regulons are sorted from most negatively associated with hazard to most positively associated with hazard.
`plotpdf` | A logical value.

### Value

A Cox hazard model plot and statistics.

### Examples

    # load survival data
    data(survival.data)

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

    stns <- tni2tnsPreprocess(stni, survivalData = survival.data,
    keycovar = c('Age','Grade'), time = 1, event = 2)
    stns <- tnsGSEA2(stns)
    stns <- tnsCox(stns, regs = c('PTTG1','E2F2','FOXM1'))
    tnsPlotCox(stns)

[Package RTNsurvival version 1.12.2 Index]