plot.bootstrap: Plot a fitted rgcca_bootstrap object

In Tenenhaus/RGCCA: Regularized (or Sparse) Generalized Canonical Correlation Analysis (R/SGCCA) for multi-block data analysis

Plot a fitted rgcca_bootstrap object

Description

Plot the results of a fitted rgcca_bootstrap object. Each block variable is shown along with its associated bootstrap confidence interval and stars reflecting the p-value of assigning a strictly positive or negative weight to this block variable.

Usage

## S3 method for class 'bootstrap'
plot(
  x,
  block = seq_along(x$rgcca$call$blocks),
  comp = 1,
  type = "weights",
  empirical = TRUE,
  n_mark = 30,
  display_order = TRUE,
  show_stars = TRUE,
  title = NULL,
  cex = 1,
  cex_sub = 12 * cex,
  cex_main = 14 * cex,
  cex_lab = 12 * cex,
  cex_point = 3 * cex,
  colors = NULL,
  adj.method = "fdr",
  ...
)

Arguments

x	A fitted rgcca_bootstrap object (see rgcca_bootstrap)
block	A numeric corresponding to the block(s) to plot.
comp	A numeric vector indicating the component(s) to consider.
type	Character string indicating the bootstrapped object to plot: block-weight vectors ("weights", default) or block-loading vectors ("loadings").
empirical	A logical value indicating if the bootstrap confidence intervals and p-values are derived from the empirical distribution. (defaut: TRUE)
n_mark	An integer defining the maximum number of variables plotted.
display_order	A logical value for ordering the variables. If TRUE, variables are ordered from highest to lowest absolute value. If FALSE, the block order is used. Default is TRUE.
show_stars	A logical for showing significance levels.
title	A character string giving the title of the plot.
cex	A numeric defining the size of the objects in the plot. Default is one.
cex_sub	A numeric defining the font size of the subtitle. Default is 12 * cex.
cex_main	A numeric defining the font size of the title. Default is 14 * cex.
cex_lab	A numeric defining the font size of the labels. Default is 12 * cex.
cex_point	A numeric defining the font size of the points. Default is 3 * cex.
colors	Colors used in the plots.
adj.method	Character string indicating the method used to adjust for p-values. It must be a method handled by the p.adjust function. Default is "fdr".
...	Additional graphical parameters.

Value

A ggplot2 plot object.

Examples

data("Russett")
blocks <- list(
  agriculture = Russett[, seq(3)],
  industry = Russett[, 4:5],
  politic = Russett[, 6:11]
)
fit.rgcca <- rgcca(blocks, ncomp = 2, method = "rgcca", tau = 1)
fit.boot <- rgcca_bootstrap(fit.rgcca, n_boot = 20, n_cores = 1)
plot(fit.boot, type = "weight", block = 1, comp = 1)

Tenenhaus/RGCCA documentation built on March 16, 2023, 2:04 p.m.