tnsPlotCox,TNS-method {RTNsurvival} | R Documentation |
Plot results from the 'tnsCox' function.
## S4 method for signature 'TNS' tnsPlotCox( tns, regs = NULL, pValueCutoff = 1, 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 )
tns |
A TNS object, which must have passed GSEA2 analysis. |
regs |
An optional string vector specifying regulons to make the plot. |
pValueCutoff |
An numeric value. The p-value cutoff applied to the results from the Cox analysis pipeline. |
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 associatedwith hazard to most positively associated with hazard. |
plotpdf |
A logical value. |
A Cox hazard model plot and statistics.
# 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)