genphen (version 1.0.0)

plotManhattan: Visualizing genphen results with Manhattan plots

Description

This procedure plots the results obtained using runGenphenSnp or runGenphenSaap.

Usage

plotManhattan(genphen.results)

Arguments

genphen.results

Data.frame resulting from runGenphenSnp or runGenphenSaap.

Value

plot

ggplot plot object.

Details

This procedure plots the results obtained using runGenphenSnp or runGenphenSaap. Each result entry is plotted as a point with respect to its effect size and classification accuracy attributes, whereby the color of the points is directly proportional to the classification accuracy. The region in the top-right corner of the plot is where the genotypes which have the strongest association with the phenotype are found.

See Also

runGenphenSaap, runGenphenSnp, plotGenphenResults, plotSpecificGenotype

Examples

#Example 1:
data(genotype.snp)
#or data(genotype.snp.msa) in this case you cannot subset genotype.snp[, 1:5]
data(phenotype.snp)
genphen.results <- runGenphenSnp(genotype = genotype.snp[, 1:5],
phenotype = phenotype.snp, technique = "svm", fold.cv = 0.66, boots = 100)
manhattan.plot <- plotManhattan(genphen.results = genphen.results)

#Example 2:
data(genotype.saap)
#or data(genotype.saap.msa) in this case you cannot subset genotype.saap[, 1:5]
data(phenotype.saap)
genphen.results <- runGenphenSaap(genotype = genotype.saap[, 1:5],
phenotype = phenotype.saap, technique = "svm", fold.cv = 0.66, boots = 100)
manhattan.plot <- plotManhattan(genphen.results = genphen.results)