Visualizing the genphen results of runGenphenRf or runGenphenSvm

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Description

This procedure visualizes the results obtained using the functions runGenphenRf or runGenphenSvm.

Usage

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plotGenphenRfSvm(genphen.results)

Arguments

genphen.results

data.frame resulting from runGenphenRf/runGenphenSvm.

Details

This procedure plots the results of the functions runGenphenRf or runGenphenSvm. Each association is shown as a point with respect to its effect size (Cohen's d) and the classification accuracy (CA). The colors of the points correspond to the Cohen's kappas. The confidence intervals estimated for the CA point estimates are provided here as well.

Value

plot

ggplot plot object.

Author(s)

Simo Kitanovski <simo.kitanovski@uni-due.de>

See Also

runGenphenRf, runGenphenSvm, plotGenphenBayes, plotSpecificGenotype, plotManhattan

Examples

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#Example 1 (RF results):
data(genotype.snp)
#or data(genotype.snp.msa) in this case you cannot subset genotype.snp[, 1:5]
data(phenotype.snp)
genphen.rf <- runGenphenRf(genotype = genotype.snp[, 1:5],
                           phenotype = phenotype.snp,
                           cv.fold = 0.66,
                           cv.steps = 100,
                           hdi.level = 0.99,
                           ntree = 1000)
plotGenphenRfSvm(genphen.results = genphen.rf)