plot_variance_explained_by_covariates {MOFA2} | R Documentation

## Plot variance explained by the smooth components of the model

### Description

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.

### Usage

    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
    )

### Arguments

`object` | a `MOFA` object
`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).

### Details

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`

### Value

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.

### Examples

    # 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)

[Package MOFA2 version 1.4.0 Index]