Contents

visualize$genome$concordance

Cross-trait directional concordance track

Renders a concordance PolyGeniusGenomeSignal as a signed genome track: one point per variant at the consensus S = value.num / value.den in [-1, 1], coloured on a diverging ramp and sized by n.models. Points near +/-1 are loci where the carrying models agree on effect direction; the shaded band over [-0.25, 0.25] marks split loci, candidates for antagonistic pleiotropy.

Usage

visualize.genome.concordance(
  signal,
  palette = NULL,
  raster = FALSE,
  raster.args = list(),
  point.alpha = 0.8,
  height = 2,
  theme = c("polygenius", "none")
)

Arguments

Argument	Description
`signal`	A PolyGeniusGenomeSignal with metadata$statistic == "concordance", from [compute$genome$concordance()](/reference/compute-genome-concordance/); any other statistic aborts, naming the producer to call. Reads chr, position, value.num, value.den and n.models from $results.
`palette`	Character vector of two or more colours, a single colour or role/hue name, a colorRampPalette-style ramp function, or NULL (default). Diverging ramp for S; NULL uses the package diverging ramp.
`raster`	Logical scalar, default FALSE. Draw the points with ggrastr::geom_point_rast() for genome-scale point counts; falls back to geom_point() with a warning when ggrastr is not installed.
`raster.args`	Named list, default list(). Extra arguments forwarded to ggrastr::geom_point_rast(), over a default raster.dpi = 300.
`point.alpha`	Numeric scalar in [0, 1], default 0.8. Point alpha.
`height`	Numeric scalar, default 2. Relative panel height when stacked.
`theme`	One of "polygenius" (default), "none". Plot theme. "none" gives a bare theme_minimal() to style yourself; palette colors are applied either way.

Value

A PolyGeniusGenomeTrack: the render spec (mark, data, params, positions, height, label, build), with build taken from signal$metadata$build. Prints as a standalone plot and composes with neither + nor draw(); stack it with visualize$genome$stack.

Details

Axis and legend labels follow the anchor the signal recorded (metadata$anchor, else diagnostics$anchor, else "none"): protective/risk for "outcome", opposes/agrees against the recorded reference model for "reference", and agree (-)/agree (+) for "none", where only |S| is meaningful. S is a display division of two summed parts; no statistic is computed here.

Examples

sig <- compute$genome$concordance(models, anchor = "outcome", gwas = gwas)
visualize$genome$concordance(sig)