create.survivalplots {SIMMS}

Plots Kaplan-meier survival curves

Description

Plots Kaplan-meier survival curves for all the training & datasets, independently as well as combined training datasets cohort and validation datasets cohort. The function also plots KM survival curves for each of the top.n.features independently.

Usage

create.survivalplots(
  data.directory = ".",
  output.directory = ".",
  training.datasets = NULL,
  validation.datasets = NULL,
  top.n.features = 25,
  learning.algorithms = c("backward", "forward"),
  truncate.survival = 100,
  survtime.cutoffs = c(seq(5, 10, 1)),
  main.title = FALSE,
  KM.plotting.fun = "create.KM.plot",
  plot.univariate.data = FALSE,
  plot.multivariate.data = TRUE,
  resolution = 100
)

Arguments

data.directory

Path to the directory containing datasets as specified by training.datasets, validation.datasets

output.directory

Path to the output folder where intermediate and results files were saved

training.datasets

A vector containing names of training datasets

validation.datasets

A vector containing names of validation datasets

top.n.features

A numeric value specifying how many top ranked features will be used for univariate survival modelling

learning.algorithms

A character vector specifying which learning algorithm to be used for model fitting and feature selection. Defaults to c('backward', 'forward'). Available options are: c('backward', 'forward', 'glm', 'randomforest')

truncate.survival

A numeric value specifying survival truncation in years. Defaults to 100 years which effectively means no truncation

survtime.cutoffs

A vector containing survival cutoff time points to be used for dichotomization of patients into risk groups for senstivity analysis

main.title

A logical to specify plot's main title. Defaults to FASLE

KM.plotting.fun

A string containing the name of the method to use for plotting KM curves. Defaults to create.KM.plot

plot.univariate.data

Logical to indicate whether to plot univariate results for all subnetworks. Default to FALSE

plot.multivariate.data

Logical to indicate whether to plot multivariate results for all subnetworks. Defaults to TRUE

resolution

A numeric value specifying resolution of the png images of KM survival curves. Defaults to 100

Value

The KM survival curves are stored under output.directory/graphs/

Author(s)

Syed Haider

Examples

# see package's main documentation