km.plot {figuRes2}

km.plot

Description

A function for creating harmonized Kaplan-Meier plots and accompanying At Risk table.

Usage

km.plot(
  parent.df,
  censor.col = "CENSOR",
  centime.col = "CENTIME.DAY",
  category.col = "REGION",
  category.palette = rainbow(5),
  at.risk.palette = rainbow(5),
  category.label = "Treatment Group",
  nsubj.plot.label = "Number at Risk",
  linetype.palette = 1:6,
  x.label = "Time Since Randomization",
  y.label = "Percetage of Subjects",
  x.limits = c(0, 48),
  x.ticks = seq(0, 48, 3),
  y.ticks = seq(0, 0.01, 0.005),
  y.limits = c(0, 0.01),
  line.size = 0.75,
  fromthetop = FALSE,
  text.size = 4
)

Arguments

parent.df

data.frame used by ggplot

censor.col

name of parent.df column associated with censor variable

centime.col

name of parent.df column associated with censored time

category.col

data.frame column associated with categorical variable (bar.plot, box.plot, cdf.plot, dot.plot, km.plot)

category.palette

colors assoicated with categorical variable

at.risk.palette

colors to be assocated with categorical variable in accompanying km.plot generated at.risk table

category.label

passed to x-axis label

nsubj.plot.label

used in km.plot

linetype.palette

values passed to scale_linetype_manual

x.label

value gets passed to labs

y.label

value gets passed to labs

x.limits

value gets passed to scale_x_continuous

x.ticks

value gets passed to scale_x_continuous

y.ticks

passed to scale_y_continuous

y.limits

passed to scale_y_continuous

line.size

value gets passed to size within geom_line, geom_step

fromthetop

logical. If TRUE KM curve decends from 1, if FALSE KM curve ascends from 0 Ensure you have an appropriate censor.col passed above!

text.size

value gets passed to geom_text

Value

A ggplot object is returned.

Author(s)

Greg Cicconetti

See Also

sync.ylab.widths, nsubj.plot

Examples

{
require(ggplot2); require(gridExtra)
data(km.data)
working.df <- km.data
head(working.df)
km.M <- km.plot(parent.df = subset(working.df, SEX== "M"),
      centime.col = "CENTIME.DAY",
      category.col = "TRTGRP",
      category.palette = c("red", "blue"),
      at.risk.palette = c("red","blue"),              
      linetype.palette = c("solid","dotted"), 
      y.limits=c(0,.01), 
      y.ticks=seq(0,.01,.005), 
      x.limits=c(-3,48),
      x.ticks=seq(0,48,6))
print(km.M[[1]])
print(km.M[[2]])
grid.arrange(km.M[[1]] + theme(legend.position= "bottom"), km.M[[2]], ncol=1)
comeback <- sync.ylab.widths(list(km.M[[1]]+ theme(legend.position= "bottom"), km.M[[2]]))
grid.arrange(comeback[[1]] , comeback[[2]], ncol=1)
build.page(interior.h = c(.8, .2),
      interior.w = c(1),
       ncol=1, nrow=2,
       interior = list(comeback[[1]], 
           comeback[[2]]))
}