HMP/U01 Coarsened Giant-Component Graph

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% relative-abundance plus PCA branch 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.

Source

Derived from the publicly available HMP+U01 16S amplicon analysis workflow used in the chm_paper project. Raw bundled artifacts and a provenance note are available under inst/extdata/hmp_u01_gc_coarse/.

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$adj_list)
#> [1] 1828
head(hmp.u01.gc.coarse$vertex_data[, c("vertex_id", "size", "cst", "subcst")])
#>    vertex_id size  cst subcst
#> 1 super_0001    4  III  III-B
#> 2 super_0002    4 IV-C  IV-C3
#> 3 super_0003    4 IV-B   IV-B
#> 4 super_0004    4 IV-A   IV-A
#> 5 super_0005    4    V      V
#> 6 super_0006    3    I    I-B