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Plot various parameters with no comp

plot_ica_ncomp_params.Rd

Helper function to plot various parameters with the no of components. You have:

  • Median stability - The median stability of the clusters at this no of components given random initialisations.

  • % Converged - The percentage of ICA runs that converged at this no of components.

  • IC Orthogonality - The orthogonality (measured as 1 - abs(cos)) indicating how orthogonal the signals detected at this level are.

  • Combined score - The product of the three other scores.

If found, the function will also add the optimal number of components based on ica_optimal_ncomp() (if a loess function could be fitted).

Usage

plot_ica_ncomp_params(object)

Arguments

object

The class, see BulkCoExp(). You need to apply ica_evaluate_comp() before running this function.

Value

The plot with no comp ~ vs. various parameters.

Examples

# stability, convergence and orthogonality against ncomp
mat <- t(synthetic_signal_matrix()$mat)
obj <- BulkCoExp(mat, data.table::data.table(sample_id = rownames(mat)))
obj <- preprocess_bulk_coexp(obj, hvg = 0.3, .verbose = FALSE)
obj <- ica_processing(obj, .verbose = FALSE)
obj <- ica_evaluate_comp(
  obj,
  ica_type = "logcosh",
  ncomp_params = params_ica_ncomp(custom_seq = seq(2L, 20L, by = 2L)),
  .verbose = FALSE
)
plot_ica_ncomp_params(obj)