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.
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