Plot Top Variants by Priority Rank

Ranked bar chart of the top variants by priority_rank, the mean percentile across the criteria selected in av_prioritize (strength, specificity, evidence breadth). Bars on the Pareto front (variants not dominated on every criterion at once) are highlighted. Unlike a calibrated score, priority_rank orders variants without claiming a unit; the Pareto highlight marks the weight-free defensible shortlist.

Usage

av_plot_priority(
  obj,
  top_n = 20L,
  show_pareto = TRUE,
  orientation = c("horizontal", "vertical")
)

Arguments

obj

An AlphaVarSet object with a priority_rank column in obj$stats$prioritization[["variant_id"]].

top_n

Integer. Number of top-ranked variants to display (default: 20).

show_pareto

Logical. Highlight bars on the Pareto front (default: TRUE).

orientation

Either "horizontal" (default, variants on the y-axis) or "vertical" (variants on the x-axis).

Value

A ggplot2 object.

Details

Requires that av_prioritize has populated obj$stats$prioritization[["variant_id"]].

Interpretation

priority_rank is a transparent equal-weighted rank, not a calibrated score: it orders variants, it does not quantify effect. Pareto-highlighted variants are the defensible shortlist: no other variant beats them on every criterion at once. The subtitle reports how many of the total variants are shown.

See also

av_prioritize, av_plot_specificity

Examples

example_file <- system.file("extdata", "bcl11a_rs1427407_example.csv",
                            package = "AlphaVaR")
obj <- av_import_csv(example_file)
#> Reading bcl11a_rs1427407_example.csv ...
obj <- av_prioritize(obj)
#> Warning: av_calc_specificity: dropped 4/2676 rows with NA in quantile_score, biosample_name, or variant_id.
av_plot_priority(obj)