plot_variance_explained_by_covariates | R Documentation |
This function plots the variance explained by the smooth components (Gaussian processes) underlying the factors in MEFISTO across different views and groups, as specified by the user.
plot_variance_explained_by_covariates(
object,
factors = "all",
x = "view",
y = "factor",
split_by = NA,
min_r2 = 0,
max_r2 = NULL,
compare_total = FALSE,
legend = TRUE
)
object |
a |
factors |
character vector with a factor name(s), or numeric vector with the index(es) of the factor(s). Default is "all". |
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"). |
min_r2 |
minimum variance explained for the color scheme (default is 0). |
max_r2 |
maximum variance explained for the color scheme. |
compare_total |
plot corresponding variance explained in total in addition |
legend |
logical indicating whether to add a legend to the plot (default is TRUE). |
Note that this function requires the use of MEFISTO.
To activate the functional MEFISTO framework, specify mefisto_options when preparing the training using prepare_mofa
A list of ggplot
objects (if compare_total
is TRUE) or a single ggplot
object.
Consider using cowplot::plot_grid(plotlist = ...) to combine the multiple plots that this function generates.
# load_model
file <- system.file("extdata", "MEFISTO_model.hdf5", package = "MOFA2")
model <- load_model(file)
plot_variance_explained_by_covariates(model)
# compare to toal variance explained
plist <- plot_variance_explained_by_covariates(model, compare_total = TRUE)
cowplot::plot_grid(plotlist = plist)
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