create.survivalplots: Plots Kaplan-meier survival curves

In SIMMS: Subnetwork Integration for Multi-Modal Signatures

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

SIMMS documentation built on April 24, 2022, 5:06 p.m.