R/validate_associations_mkg.R
validate_associations_mkg.RdThis function validates the associations between phenotypes and cell types with the Monarch Knowledge Graph (MKG). It computes the number of phenotypes and cell types that are present in the MKG and the number of associations that are present in the MKG.
validate_associations_mkg(
results = load_example_results(),
kg = get_data("monarch_kg_cells.csv"),
q_threshold = 0.05,
cl = KGExplorer::get_ontology(name = "cl", remove_cyclic_paths = TRUE, remove_rings =
TRUE),
alt_ids = c(`CL:0000111` = "CL:2000032"),
metric = c("dist_nca.min_adj", "dist_lca.min_adj", "dist_nca.min", "dist_lca.min")[1]
)The cell type-phenotype enrichment results generated by gen_results and merged together with merge_results
A data.table with phenotype-cell type relationships ("from" and "to" columns, respectively) gathered from the Monarch Knowledge Graph.
The q value threshold to subset the results by.
Cell Ontology object.
Alternative IDs to map CL IDs into.
Ontological distance metric to use for plotting.
results <- load_example_results()
kg <- validate_associations_mkg(result=results)
#> Adding logFC column.
#> ℹ All local files already up-to-date!
#> Remaining: 82 phenotypes across 65 celltypes.
#> 90.24% phenotypes recovered.
#> Mapping cell types to cell ontology terms.
#> Adding stage information.
#> [i=1] cl_id: CL:0000000 & hpo_id: HP:0025354
#> Loading cached ontology: /github/home/.cache/R/KGExplorer/cl.rds
#> [i=2] cl_id: CL:0000000 & hpo_id: HP:0005374
#> [i=3] cl_id: CL:0000015 & hpo_id: HP:0012863
#> [i=4] cl_id: CL:0000019 & hpo_id: HP:0000027
#> [i=5] cl_id: CL:0000019 & hpo_id: HP:0012864
#> [i=6] cl_id: CL:0000038 & hpo_id: HP:0012131
#> [i=7] cl_id: CL:0000066 & hpo_id: HP:0032599
#> [i=8] cl_id: CL:0000084 & hpo_id: HP:0002843
#> [i=9] cl_id: CL:0000084 & hpo_id: HP:0011840
#> [i=10] cl_id: CL:0000094 & hpo_id: HP:0001911
#> [i=11] cl_id: CL:0000097 & hpo_id: HP:0100494
#> [i=12] cl_id: CL:0000100 & hpo_id: HP:0002450
#> [i=13] cl_id: CL:2000032 & hpo_id: HP:0003134
#> [i=14] cl_id: CL:0000125 & hpo_id: HP:0100705
#> [i=15] cl_id: CL:0000127 & hpo_id: HP:0100707
#> [i=16] cl_id: CL:0000128 & hpo_id: HP:0100706
#> [i=17] cl_id: CL:0000169 & hpo_id: HP:0006279
#> [i=18] cl_id: CL:0000169 & hpo_id: HP:0006274
#> [i=19] cl_id: CL:0000178 & hpo_id: HP:0010789
#> [i=20] cl_id: CL:0000182 & hpo_id: HP:0031137
#> [i=21] cl_id: CL:0000187 & hpo_id: HP:0100299
#> [i=22] cl_id: CL:0000188 & hpo_id: HP:0004303
#> [i=23] cl_id: CL:0000232 & hpo_id: HP:0001876
#> [i=24] cl_id: CL:0000232 & hpo_id: HP:0001877
#> [i=25] cl_id: CL:0000232 & hpo_id: HP:0410064
#> [i=26] cl_id: CL:0000232 & hpo_id: HP:0410063
#> [i=27] cl_id: CL:0000232 & hpo_id: HP:0020054
#> [i=28] cl_id: CL:0000232 & hpo_id: HP:0012187
#> [i=29] cl_id: CL:0000233 & hpo_id: HP:0001872
#> [i=30] cl_id: CL:0000235 & hpo_id: HP:0004311
#> [i=31] cl_id: CL:0000236 & hpo_id: HP:0005372
#> [i=32] cl_id: CL:0000236 & hpo_id: HP:0002846
#> [i=33] cl_id: CL:0000492 & hpo_id: HP:0500267
#> [i=34] cl_id: CL:0000540 & hpo_id: HP:0002493
#> [i=35] cl_id: CL:0000540 & hpo_id: HP:0002529
#> [i=36] cl_id: CL:0000540 & hpo_id: HP:0012757
#> [i=37] cl_id: CL:0000542 & hpo_id: HP:0004332
#> [i=38] cl_id: CL:0000547 & hpo_id: HP:0025035
#> [i=39] cl_id: CL:0000556 & hpo_id: HP:0012143
#> [i=40] cl_id: CL:0000576 & hpo_id: HP:0012144
#> [i=41] cl_id: CL:0000586 & hpo_id: HP:0012862
#> [i=42] cl_id: CL:0000623 & hpo_id: HP:0012177
#> [i=43] cl_id: CL:0000623 & hpo_id: HP:0012176
#> [i=44] cl_id: CL:0000624 & hpo_id: HP:0031392
#> [i=45] cl_id: CL:0000625 & hpo_id: HP:0031393
#> [i=46] cl_id: CL:0000738 & hpo_id: HP:0008318
#> [i=47] cl_id: CL:0000738 & hpo_id: HP:0004852
#> [i=48] cl_id: CL:0000738 & hpo_id: HP:0001881
#> [i=49] cl_id: CL:0000763 & hpo_id: HP:0020047
#> [i=50] cl_id: CL:0000764 & hpo_id: HP:0012130
#> [i=51] cl_id: CL:0000765 & hpo_id: HP:0034278
#> [i=52] cl_id: CL:0000766 & hpo_id: HP:0010974
#> [i=53] cl_id: CL:0000767 & hpo_id: HP:0001912
#> [i=54] cl_id: CL:0000771 & hpo_id: HP:0001879
#> [i=55] cl_id: CL:0000775 & hpo_id: HP:0001874
#> [i=56] cl_id: CL:0000787 & hpo_id: HP:0030373
#> [i=57] cl_id: CL:0000792 & hpo_id: HP:0020111
#> [i=58] cl_id: CL:0000798 & hpo_id: HP:0500270
#> [i=59] cl_id: CL:0000813 & hpo_id: HP:0032182
#> [i=60] cl_id: CL:0000818 & hpo_id: HP:0030379
#> [i=61] cl_id: CL:0000835 & hpo_id: HP:0004808
#> [i=62] cl_id: CL:0000845 & hpo_id: HP:0030383
#> [i=63] cl_id: CL:0000891 & hpo_id: HP:0003651
#> [i=64] cl_id: CL:0000895 & hpo_id: HP:0410373
#> [i=65] cl_id: CL:0000898 & hpo_id: HP:0031396
#> [i=66] cl_id: CL:0000909 & hpo_id: HP:0410380
#> [i=67] cl_id: CL:0000912 & hpo_id: HP:0500263
#> [i=68] cl_id: CL:0000972 & hpo_id: HP:0030386
#> [i=69] cl_id: CL:0001050 & hpo_id: HP:0410395
#> [i=70] cl_id: CL:0001062 & hpo_id: HP:0020177
#> [i=71] cl_id: CL:0002092 & hpo_id: HP:0005561
#> [i=72] cl_id: CL:0002191 & hpo_id: HP:0012135
#> [i=73] cl_id: CL:0002198 & hpo_id: HP:0005152
#> [i=74] cl_id: CL:0002319 & hpo_id: HP:0002282
#> [i=75] cl_id: CL:0002368 & hpo_id: HP:0012261
#> [i=76] cl_id: CL:0002422 & hpo_id: HP:0004312
#> [i=77] cl_id: CL:0002559 & hpo_id: HP:0500262
#> [i=78] cl_id: CL:0008002 & hpo_id: HP:0030089
#> [i=79] cl_id: CL:0008002 & hpo_id: HP:0003713
#> [i=80] cl_id: CL:0008002 & hpo_id: HP:0012084
#> [i=81] cl_id: CL:0011001 & hpo_id: HP:0006802
#> [i=82] cl_id: CL:0011025 & hpo_id: HP:0041080