pairsInfo-methods: Plot an INFO metric on a genomic axis.
In kevinrue/TVTB: TVTB: The VCF Tool Box

Description Usage Arguments Value Author(s) See Also Examples

Make a matrix of plots that display a metric calculated in levels of a given phenotype, and stored in columns of the info slot of a VCF object.

1 2	## S4 method for signature 'VCF' pairsInfo(vcf, metric, phenotype, ..., title = metric)

`vcf`	`VCF` object.
`metric`	Metric to plot on the Y axis. All columns in the `info` slot of hte `vcf` object that match the pattern `"phenotype_(.*)_metric"` are plotted in the `DataTrack`. An error is thrown if no such column is found.
`phenotype`	Column in the `phenoData` slot of the `vcf` object. Levels of this phenotype are plotted and contrasted in the `DataTrack`. See argument `metric` for details.
`...`	Additional arguments, passed to the `ggpairs` method.
`title`	Title for the graph, passed to the `ggpairs` method.

gg object returned by the ggpairs method.

Kevin Rue-Albrecht

ggpairs, addPhenoLevelFrequencies,ExpandedVCF-method, and VCF.

# Example data ----

# VCF file
vcfFile <- system.file("extdata", "moderate.vcf", package = "TVTB")

# Phenotype file
phenoFile <- system.file("extdata", "moderate_pheno.txt", package = "TVTB")
phenotypes <- S4Vectors::DataFrame(read.table(phenoFile, TRUE, row.names = 1))

# TVTB parameters
tparam <- TVTBparam(Genotypes("0|0", c("0|1", "1|0"), "1|1"))

# Pre-process variants
vcf <- VariantAnnotation::readVcf(
    vcfFile, param = tparam, colData = phenotypes)
vcf <- VariantAnnotation::expand(vcf, row.names = TRUE)
vcf <- addFrequencies(vcf, "super_pop")

# Example usage ----

pairsInfo(vcf, "MAF", "super_pop")