plot_pareto: Plot pareto front from an galgo.Obj

Description Usage Arguments Value Examples

View source: R/plot-functions.R

Description

Plot pareto front from an galgo.Obj

Usage

1
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

 1
 2
 3
 4
 5
 6
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
# 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/galgoR-package documentation built on Oct. 26, 2020, 7:05 a.m.