Converts hypergraph incidence matrix to long-format data frame for analysis and visualization.
Usage
tidy(x, ...)
# S4 method for class 'MultiWayContacts'
tidy(x, max_hyperedges = NULL, weight_normalization = "none")Arguments
- x
MultiWayContacts with built hypergraph.
- ...
Additional arguments (not used).
- max_hyperedges
Integer or NULL. Maximum hyperedges to include (default: NULL for all). Selects top by contact order.
- weight_normalization
Character. Weight scheme:
"none"(raw),"log","by_order", or"minmax"(default:"none").
Value
MultiWayContacts with tidied_hypergraph slot containing: bin_idx,
hyperedge_idx, bin_id, chrom, bin, n_multiways, weight.
Details
Converts sparse matrix to long format. When max_hyperedges is set, ranks
by contact order and retains top N. Unused bins are removed.
Examples
if (FALSE) { # \dontrun{
# Tidy all with raw weights
mc <- MultiWayContacts("sample.pairs.gz") |> import() |> build() |> tidy()
# Top 100 with log weights
mc <- mc |> tidy(max_hyperedges = 100, weight_normalization = "log")
} # }