visualize

Visualization functions for PolyGenius

Description

visualize is an environment that bundles visualization helpers for PolyGenius objects and analysis results.

The rationale is to keep visual access close to the domain object being inspected:

  • visualize$data for cohort-linked score and embedding views,

  • visualize$associations for association outputs, and

  • visualize$evaluate for performance, comparison, and relationship plots.

This mirrors the high-level PolyGenius workflow: compute or generate results first, then visualize the resulting object directly rather than reconstructing plotting inputs manually.

It provides:

Data plots (visualize$data):

  • scores$distribution() – Score distributions across samples/groups

  • scores$distribution.heatmap() – Model-by-distribution score heatmaps

  • scores$heatmap() – Samples-by-models score heatmaps

  • similarity$obs() – Heatmaps for pre-computed similarity matrices

  • similarity$mod() – Model similarity heatmaps

  • embedding$obs() – Scatter plots for dimensionality reduction results

  • embedding$mod() – Model embedding scatter plots

Association plots (visualize$associations):

  • forest() – Forest plots for association results

  • heatmap() – Heatmaps of associations across outcomes/predictors

  • survival() – Survival curves stratified by PRS

Evaluation plots (visualize$evaluate):

  • leaderboard() – Cross-metric evaluation leaderboard heatmap

  • discrimination$roc() / discrimination$pr() / discrimination$confusion()

  • discrimination$distribution() / discrimination$predicted.vs.observed() / discrimination$residuals()

  • calibration$curve() / calibration$slope.intercept()

  • compare$delta.forest() / compare$delta.heatmap()

  • similarity$heatmap() – Model-model relationship heatmaps

  • incremental$delta()

  • risk.strata$profile() / risk.strata$lift()

  • diagnostics$metric.flags()

Visualization functions return display-ready plot objects, typically ggplot2 plots or ComplexHeatmap heatmaps depending on the plotting backend used by the specific function.

Usage

visualize

Format

An object of class visualizeEngine (inherits from environment) of length 3.