Plot PCA loadings — hd_plot_pca_loadings • HDAnalyzeR

hd_plot_pca_loadings() plots the PCA loadings for the top n features and first m PCs. n and m are defined by the user. The contribution direction of the features is indicated by the color of the bars.

Usage

hd_plot_pca_loadings(pca_object, displayed_pcs = 6, displayed_features = 15)

Arguments

pca_object: A PCA object containing the PCA loadings. Created by hd_pca().
displayed_pcs: The number of PCs to be displayed. Default is 6.
displayed_features: The number of features to be displayed. Default is 15.

Value

A ggplot object

Examples

# Create the HDAnalyzeR object providing the data and metadata
hd_object <- hd_initialize(example_data, example_metadata)

# Run the PCA analysis and create the loadings plot
pca_object <- hd_pca(hd_object, components = 5, by_sample = TRUE, seed = 123) |>
  hd_plot_pca_loadings()

pca_object$pca_loadings_plot