BEAMR (version 1.1.0)

plot_beam_boot: Plot bootstrap output for BEAM sets

Description

#' plot_beam_boot produces a pairs plot of the beam stats matrices. Default is maximum of 5 plots, ordered by most significant association direction.

Usage

plot_beam_boot(
  beam.result,
  beam.feat.pvals,
  beam.specs = NULL,
  set.id,
  max.plots = 4,
  z = TRUE
)

Value

A pairs plot figure.

Arguments

beam.result

A beam.stats object from compute_beam_stats

beam.feat.pvals

A list containing feature-level p-values from compute_feature_pvalues.

beam.specs

A data.frame. Default NULL, in which case beam.result$beam.specs is used. Otherwise can input other beam.specs data.frame that must contain name, mtx, mdl, plot columns.

set.id

A character specifying the name of a set. Must be in beam.result$beam.data$set.data

max.plots

A number specifying the max number of rows in the pairs plot. Default is 4, ordered by feature-level p-value.

z

Logical indicating whether to z-scale each vector of one coefficient estimate across bootstraps before plotting. Default is TRUE.

Examples

data(beam_stats)
test.pvals <- compute_set_pvalues(beam.stats=beam_stats)
test.feat.pvals <- compute_feature_pvalues(beam.stats=beam_stats)
test.boot.plot <- plot_beam_boot(beam_stats, test.feat.pvals,
                                 set.id="ENSG00000099810")