Get correlation-based graph — get_cor

Helper function to get a correlation-based igraph from the class

Usage

get_cor_graph(object, epsilon, .verbose)

Arguments

object: The class, see BulkCoExp().
epsilon: Float. The epsilon parameter for the RBF function, in this case the bump function.
.verbose: Boolean. Controls verbosity of the function.

Value

A list with the following elements:

graph - The igraph
params - A list that contains the parameters of the graph generation and general graph information (node, edge numbers).

Examples

# igraph from the stored correlations at a fixed epsilon
mat <- t(synthetic_signal_matrix()$mat)
obj <- BulkCoExp(mat, data.table::data.table(sample_id = rownames(mat)))
obj <- preprocess_bulk_coexp(obj, hvg = 0.3, .verbose = FALSE)
obj <- cor_module_processing(obj, cor_method = "spearman", .verbose = FALSE)
graph_res <- get_cor_graph(obj, epsilon = 2, .verbose = FALSE)
graph_res$params
#> $epsilon
#> [1] 2
#> 
#> $no_nodes
#> [1] 217
#> 
#> $no_edges
#> [1] 4833
#>