Plots features weight in/not in a set — plot_features_weight

Plots the distribution of features weight from an integration method, depending on whether the features belong to a feature set of interest.

Usage

plot_features_weight_set(
  method_output,
  feature_set,
  set_name = "set",
  features_metric = c("signed_importance", "weight", "importance"),
  add_missing_features = FALSE,
  mo_data = NULL,
  datasets = NULL,
  latent_dimensions = NULL,
  point_alpha = 0.5,
  add_boxplot = TRUE,
  scales = "free_x"
)

Arguments

method_output: Integration method output generated via the get_output() function.
feature_set: Character vector, features ID belonging to the features set of interest.
set_name: Character, name of the set. Default value is 'set'.
features_metric: Character, the features metric that should be plotted on the y-axis. Should be one of 'signed_importance' (default value), 'weight' or 'importance'.
add_missing_features: Logical, whether features that are in a multi-omics dataset (provided through the mo_data argument) but don't have a weight in the integration results (e.g. because they were not selected in the pre-processing step) should be added in the results. If TRUE (default value), they will be added with a weight and importance of 0.
mo_data: A MultiDataSet-class object. If add_missing_features is true, all features in the multi-omics dataset with no weight in the integration method result will be added with a weight and importance of 0.
datasets: Character vector, name of the datasets for which the features importance should be plotted. If NULL (default value), all datasets will be considered.
latent_dimensions: Character vector, the latent dimensions to represent in the plot. If NULL (default value), all latent dimensions will be represented.
point_alpha: Numeric between 0 and 1, the opacity of the points in the plot (with 1 = fully opaque, and 0 = fully transparent). Default value is 0.5.
add_boxplot: Logical, should a boxplot be drawn on top of the points for categorical covariates? Default value is TRUE.
scales: Character, value to use for the scales argument of ggplot2::facet_grid(). Default value is 'free_x'.

Value

a ggplot.