grip (version 0.1.2)

hmp.u01.gc.coarse: HMP/U01 Coarsened Giant-Component Graph

Description

A bundled coarsened graph derived from the giant connected component of the HMP+U01 16S amplicon iKNN graph used in the HMP/U01 layout-selection study. The upstream graph came from the `>=1 with `k = 3`, after restricting to the biologically meaningful major component. The graph was then greedily coarsened in two rounds from `6474` vertices to `1828` supernodes.

Usage

hmp.u01.gc.coarse

Format

A named list with components:

adj_list

Adjacency list of length `1828`, with 1-based integer neighbor indices.

weight_list

Parallel list of positive edge weights.

vertex_data

Data frame with one row per coarse vertex and columns `vertex_id`, `size`, `cst`, `subcst`, `dcst.depth1.absorb`, `dcst.depth1.rare`, `dcst.depth2.absorb`, `dcst.depth2.rare`, `ph`, and `log10_reads`.

graph_info

Named list summarizing provenance and graph-level metadata, including the original and coarsened vertex counts, selected `k`, edge count, and coarsening rounds.

Details

The object is intended for examples and vignettes on real-world 3D layout comparison. It is small enough to ship with the package while preserving the arm-like graph structure that motivated the tuned preset analysis.

Examples

data(hmp.u01.gc.coarse)
length(hmp.u01.gc.coarse$adj_list)
head(hmp.u01.gc.coarse$vertex_data[, c("vertex_id", "size", "cst", "subcst")])