tnsPlotCoxInteraction,TNS-method {RTNsurvival} | R Documentation |
Plot results from Cox regression analysis for dual regulons
## 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 )
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. |
A Cox hazard model plot and statistics.
A 3D heatmap plot.
# 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")