plot_variance_explained: Plot variance explained by the model

View source: R/calculate_variance_explained.R

plot_variance_explainedR Documentation

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.