tnsPlotCoxInteraction,TNS-method {RTNsurvival} | R Documentation

## Plot results from Cox regression analysis for dual regulons

### 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")

[Package RTNsurvival version 1.12.2 Index]