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Plot Eigenvalue Scree Plot

Source: R/visualization.R
plot_eigen.Rd

Displays the top eigenvalues as a scatter plot to help visualize the spectral gap and inform dimensionality selection. The elbow in the scree plot corresponds to the rank automatically selected by find_elbow_kneedle.

Usage

plot_eigen(eigenvalues, n = NULL)

Arguments

eigenvalues

Numeric vector of eigenvalues, typically from run_MOSAIC()$eigenvalues or from a per-sample eigendecomposition.

n

Integer. Number of eigenvalues to plot. Default: min(50, length(eigenvalues)).

Value

A ggplot object that can be further customized or saved with ggsave().

See also

find_elbow_kneedle for automatic dimensionality selection from the same eigenvalues.

Examples

# Basic usage
eigenvalues <- c(10, 5, 3, 2, 1.5, 1.2, 1.1, 1.05, 1.01, 1.0)
plot_eigen(eigenvalues)


# Plot only the first 5
plot_eigen(eigenvalues, n = 5)


if (FALSE) { # \dontrun{
# After running MOSAIC
result <- run_MOSAIC(list(RNA = seurat_rna),
                     sample_meta = "sample_id",
                     condition_meta = "condition")
plot_eigen(result$eigenvalues)
} # }