surv.scale: Plots a survival color scale, for legend

In LPS: Linear Predictor Score, for Binary Inference from Multiple Continuous Variables

Description

This function plots a color scale using a custom color palette, to legend surv.colors annotations.

Usage

  surv.scale(time, event, eventColors = c("#000000", "#CCCCCC"),
    censColors = c("#FFFFEE", "#FFDD00"))

Arguments

time	Numeric vector, the follow-up times of each individual (see Surv in the survival package).
event	Logical vector, whether an event (death, relapse ...) occured at the end of each individual follow-up or not (see Surv in the survival package).
eventColors	Character vector of length 2, the boundaries of the color scale to generate for individuals with events.
censColors	Character vector of length 2, the boundaries of the color scale to generate for right-censored individuals.

Author(s)

Sylvain Mareschal

See Also

surv.colors, survival::Surv

Examples

  # Rosenwald's dataset (hand-picked prognostic probes)
  data(rosenwald)
  probes <- c("30580", "16006", "32315", "16978", "26588")
  expr <- t(rosenwald.expr[ probes ,])
  
  # NA imputation (feature's mean to minimize impact)
  f <- function(x) { x[ is.na(x) ] <- round(mean(x, na.rm=TRUE), 3); x }
  expr <- apply(expr, 2, f)
  
  # Survival colors
  surv <- with(rosenwald.cli, surv.colors(time=follow.up, event=status=="Dead"))
  
  # Annotated clustering
  side <- data.frame(OS=surv, row.names=rownames(rosenwald.cli))
  clusterize(expr, side=side)
  
  # Color scale legend
  with(rosenwald.cli, surv.scale(time=follow.up, event=status=="Dead"))

LPS documentation built on May 29, 2021, 5:07 p.m.