tnsPlotCovariates-methods: Plot regulon activity and categorical covariates

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

Description

This method plots regulon activity for a given regulon in all samples and adds covariate tracks to evaluate the regulon activity distribution. The samples are order by regulon activity for that particular regulon.

Usage

## S4 method for signature 'TNS'
tnsPlotCovariates(
  tns,
  regs = NULL,
  attribs = NULL,
  fname = "covarplot",
  fpath = ".",
  ylab = "Regulon activity (dES)",
  xlab = "Samples",
  plotpdf = FALSE,
  plotbatch = FALSE,
  panelHeights = c(1, 1),
  width = 5.3,
  height = 4,
  dummyEncode = TRUE,
  divs = NULL
)

Arguments

tns	A A TNS object.
regs	An optional string vector specifying regulons to plot.
attribs	A character vector of attributes listed in the column names of the survivalData. All attributes should be either binary encoded or categorical variables for plotting. Available attributes can be checked by running colnames(tnsGet(tns, "survivalData")). Alternatively, attributes can be grouped when provided within a list.
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
ylab	A string. The label of the y-axis, describing what is represented.
xlab	A string. The label of the x-axis.
plotpdf	A logical value. If TRUE, a pdf file is created instead of plotting to the graphics device.
plotbatch	A logical value. If TRUE, plots for all regulons are saved in the same file. If FALSE, each plot for each regulon is saved in a different file.
panelHeights	A numeric vector of length 2 specifying the relative heights of the panels (regulon activity plot, and covariate tracks)
width	A numeric value. Represents the width of the plot.
height	A numeric value. Represents the height of the plot.
dummyEncode	A logical value. If TRUE, all categorical variables are dummy encoded. If FALSE, categorical variables are represented as one track and a legend is added to the plot.
divs	A numeric vector of division positions in the covariate tracks.

Details

Automatic dummy encoding is available for categorical variables.

Value

A plot of regulon activity and covariate tracks.

Examples

 # load survival data
 data(survival.data)
 # load TNI-object
 data(stni, package = "RTN")
 
 # create TNS object
 stns <- tni2tnsPreprocess(stni, survivalData = survival.data,
 keycovar = c('Grade','Age'), time = 1, event = 2)
 stns <- tnsGSEA2(stns)
 
 # plot only binary covariates
 tnsPlotCovariates(stns, "MYB", 
 attribs = c("ER+", "ER-", "PR+", "PR-", "LumA", "LumB", "Basal", 
 "Her2", "Normal"), divs = c(2, 4))
 
 # also dummy encode categorical variables (LN and Grade)
 tnsPlotCovariates(stns, "MYB", 
 attribs = c("ER+", "ER-", "PR+", "PR-", "LumA", "LumB", "Basal", 
 "Her2", "Normal", "LN", "Grade"), divs = c(2, 4, 9, 12))
 
 # don't dummy encode categorical variables
 tnsPlotCovariates(stns, "MYB", attribs = c("ER+", "ER-", "PR+", "PR-",
 "LumA", "LumB", "Basal", "Her2", "Normal", "Grade"), divs = c(2, 4, 9),
 dummyEncode = FALSE)
 

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