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

Description Usage Arguments Value Author(s) See Also Examples

Plot, on a genomic axis, a metric calculated in levels of a given phenotype, and stored in columns of the info slot of a VCF object.

## S4 method for signature 'VCF'
plotInfo(
    vcf, metric, range, annotation, phenotype, type = c("p", "heatmap"),
    zero.rm = FALSE)

`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.
`range`	A `GRanges` of length one that defines the region to visualise. All variants in the `vcf` object overlapping this region are plotted.
`annotation`	An `EnsDb` annotation package from which to fetch gene annotations. `TxDb` packages may be supported in the future.
`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.
`type`	Plotting type(s), as listed in `DataTrack`.
`zero.rm`	If `TRUE`, values equal to `0` are not displayed in the `DataTrack`.

list returned by the plotTracks method.

Kevin Rue-Albrecht

plotTracks, 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 ----

if (requireNamespace("EnsDb.Hsapiens.v75")){
    plotInfo(
        vcf, "MAF",
        range(GenomicRanges::granges(vcf)),
        EnsDb.Hsapiens.v75::EnsDb.Hsapiens.v75,
        "super_pop"
    )
}