plot_variance_explained: Plot variance explained by the model

In bioFAM/MOFA2: Multi-Omics Factor Analysis v2

Plot variance explained by the model

Description

plots the variance explained by the MOFA factors across different views and groups, as specified by the user. Consider using cowplot::plot_grid(plotlist = ...) to combine the multiple plots that this function generates.

Usage

plot_variance_explained(
  object,
  x = "view",
  y = "factor",
  split_by = NA,
  plot_total = FALSE,
  factors = "all",
  min_r2 = 0,
  max_r2 = NULL,
  legend = TRUE,
  use_cache = TRUE,
  ...
)

Arguments

object	a MOFA object
x	character specifying the dimension for the x-axis ("view", "factor", or "group").
y	character specifying the dimension for the y-axis ("view", "factor", or "group").
split_by	character specifying the dimension to be faceted ("view", "factor", or "group").
plot_total	logical value to indicate if to plot the total variance explained (for the variable in the x-axis)
factors	character vector with a factor name(s), or numeric vector with the index(es) of the factor(s). Default is "all".
min_r2	minimum variance explained for the color scheme (default is 0).
max_r2	maximum variance explained for the color scheme.
legend	logical indicating whether to add a legend to the plot (default is TRUE).
use_cache	logical indicating whether to use cache (default is TRUE)
...	extra arguments to be passed to calculate_variance_explained

Value

A list of ggplot objects (if plot_total is TRUE) or a single ggplot object

Examples

# Using an existing trained model on simulated data
file <- system.file("extdata", "model.hdf5", package = "MOFA2")
model <- load_model(file)

# Calculate variance explained (R2)
r2 <- calculate_variance_explained(model)

# Plot variance explained values (view as x-axis, and factor as y-axis)
plot_variance_explained(model, x="view", y="factor")

# Plot variance explained values (view as x-axis, and group as y-axis)
plot_variance_explained(model, x="view", y="group")

# Plot variance explained values for factors 1 to 3
plot_variance_explained(model, x="view", y="group", factors=1:3)

# Scale R2 values
plot_variance_explained(model, max_r2=0.25)

bioFAM/MOFA2 documentation built on June 12, 2024, 3:57 p.m.