Contents
visualize$models$top.variants
Most-reused variants
Bar chart of the variants that appear in the most models, most-reused first.
Each bar is labelled with the full harmonized identifier
chr:position:ea:nea, effect allele first, so it can be looked up directly in
an external tool. The subtitle states the genome build; no table is returned.
Usage
visualize.models.top.variants(
models,
top.n = 25,
palette = NULL,
axis = c("y", "x"),
theme = c("polygenius", "none")
)Arguments
| Argument | Description |
|---|---|
models | A PGSLibrary or a single PGS. Any other class, or an empty PGS library, aborts. A set spanning two genome builds is refused by the backbone accessor. |
top.n | Numeric scalar, default 25. Number of top variants to show; fewer bars are drawn when fewer variants are carried by any model. |
palette | Bar fill: NULL (default) or a single colour (name or hex, e.g. "darkgreen") fills every bar flat; two or more colours (e.g. c("lightgrey", "darkgreen")) or a colorRampPalette-style ramp function fills them with a gradient keyed to bar height, taller bars at the high end of the ramp. Anything else aborts. See [visualize](/reference/visualize/). |
axis | One of "y" (default), "x". Which axis the variants sit on: "y" draws horizontal bars with variant labels down the y-axis, "x" draws vertical bars with variant labels along the x-axis. |
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 ggplot object, so it composes with +. Under a gradient
palette the bars are coloured by reuse count; under a flat one they share
a single fill.
Examples
visualize$models$top.variants(models, top.n = 30)
visualize$models$top.variants(models, axis = "x")See Also
visualize$models$reuse for the reuse distribution these are the tail of; visualize$genome$reuse to place them on the genome.
Other visualize-models:
visualize.models.reuse(),
visualize.models.sizes(),
visualize.models.uniqueness()