Contents
visualize$genome$coverage
Genomic coverage by the model library (distinct models per bin)
Companion coverage track to visualize$genome$effects: per genomic bin, the number of distinct models contributing a variant there. A bin that is dense here and split in effect direction in the Miami above is a candidate for antagonistic pleiotropy.
Usage
visualize.genome.coverage(
models,
min.models = 1,
binwidth = 1e+07,
reduce = c("bin", "window"),
window = NULL,
palette = NULL,
chr.colors = NULL,
height = 0.6,
theme = c("polygenius", "none")
)Arguments
| Argument | Description |
|---|---|
models | A PGSLibrary or a single PGS. Any other class, or an empty PGS library, aborts. Variants are allele-harmonized first; strand-ambiguous variants (A/T, C/G) are dropped. |
min.models | Numeric scalar, default 1. Minimum number of models a variant must appear in to be counted; below 1 aborts, as does a value no variant reaches. |
binwidth | Numeric scalar (base pairs), default 1e7 (10 Mb). Display bin width. Superseded under a region = zoom on the stack, which re-bins to about 50 bins across the visible window. |
reduce | One of "bin" (default), "window". "bin" counts distinct models per disjoint bin; "window" counts over overlapping windows, each variant's model counted in every bin within +/- window/2, clipped to its chromosome. A model is never double-counted within one bin. |
window | Numeric scalar (base pairs), or NULL (default). Smoothing width for reduce = "window"; NULL uses three times the display bin width. |
palette | Bar fill, and the flat-versus-gradient switch. NULL (default, the package colour) or a single colour (name or hex) draws flat bars alternating by chromosome in a two-tone of that colour and neutral grey, as the Manhattan track does, so stacked tracks line up. Two or more colours (e.g. c("lightgrey", "darkgreen")) or a colorRampPalette-style ramp function instead fills the bars with a gradient keyed to the models-per-bin count, denser bins at the high end of the ramp. Anything else aborts. |
chr.colors | Character vector of two colours, or NULL (default). Overrides the chromosome two-tone in flat mode (e.g. c("#045669", "#822B2A")), since palette is taken by the flat-versus-gradient choice. Ignored in gradient mode. |
height | Numeric scalar, default 0.6. Relative panel height when stacked, sizing it as a thin context rail under the signal tracks. |
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), build being the PGS library's
resolved genome build. Binning happens at render, so a region = zoom
re-bins the visible window rather than cropping whole-genome bins. Prints as
a standalone plot and composes with neither + nor draw(); stack it with
visualize$genome$stack.
Examples
visualize$genome$coverage(models, binwidth = 5e6)
visualize$genome$coverage(models, palette = c("lightgrey", "darkgreen"))See Also
visualize$genome$effects, the signal
track this rails under;
visualize$genome$cumulativeWeight for
the same bins weighted by |beta| instead of counted.
Other visualize-genome:
visualize.genome.attribution(),
visualize.genome.concordance(),
visualize.genome.convergence(),
visualize.genome.cumulativeWeight(),
visualize.genome.effects(),
visualize.genome.loci(),
visualize.genome.manhattan(),
visualize.genome.overview(),
visualize.genome.prs(),
visualize.genome.reuse(),
visualize.genome.stack()