plot_pareto: Plot pareto front from an galgo.Obj

In harpomaxx/GSgalgoR: An Evolutionary Framework for the Identification and Study of Prognostic Gene Expression Signatures in Cancer

Description

Plot pareto front from an galgo.Obj

Usage

plot_pareto(output)

Arguments

output

An object of class galgo.Obj

Value

This function returns a scatterplot showing the solutions found by Galgo accross all generations in the solution space, where the Silhouette Fitness is in the x-axis and the survival fitness in the y-axis. A line is drawn over all non-dominated solutions showing the estimated Pareto front

Examples

# load example dataset
library(breastCancerTRANSBIG)
data(transbig)
Train <- transbig
rm(transbig)

expression <- Biobase::exprs(Train)
clinical <- Biobase::pData(Train)
OS <- survival::Surv(time = clinical$t.rfs, event = clinical$e.rfs)

# We will use a reduced dataset for the example
expression <- expression[sample(1:nrow(expression), 100), ]

# Now we scale the expression matrix
expression <- t(scale(t(expression)))

# Run galgo
output <- GSgalgoR::galgo(generations = 5, population = 15, 
prob_matrix = expression, OS = OS)
plot_pareto(output)

harpomaxx/GSgalgoR documentation built on Oct. 25, 2020, 3:47 p.m.