Contents

visualize$genome$loci

Genomic loci track

A thin track of labelled rectangles, one per interval, for marking hotspots or candidate regions above the data tracks of a visualize$genome$stack. To shade the same intervals through every panel, pass them to the stack as bands = as well.

Usage

visualize.genome.loci(regions, label = TRUE, height = 0.3)

Arguments

Argument	Description
`regions`	A character vector of "chr:start-end" strings, or a data frame with chr, start, end and an optional label column. A data-frame row with start == end, such as a lead variant, is read as one base. A malformed row aborts naming its index.
`label`	Logical scalar, default TRUE. Label each rectangle with its label, or chr:start-end when there is none.
`height`	Numeric scalar, default 0.3. Relative panel height when stacked.

Value

A PolyGeniusGenomeTrack with build NA, compatible with a track of any build. Its loci also enter the stack's shared axis.

Details

A locus is kept under a region = zoom whenever it overlaps the window, so one straddling a zoom edge is drawn clipped rather than dropped. Each rectangle is drawn at least 0.3% of the visible span wide, so a locus far narrower than a pixel at genome scale stays visible. That widening is display only.

Examples

hotspots <- data.frame(chr = c("17", "19"), start = c(45.5e6, 44.4e6),
                       end = c(46.5e6, 45.4e6), label = c("MAPT", "APOE"))
tr <- visualize$genome$loci(hotspots)