vignettes/pathway.Rmd
pathway.Rmd
searchPath(graph, ec ~ kegg_path, include = "kegg_rxn", k = 3)
#> Path 1:
#> ec -(KEGG)-> kegg_rxn -(KEGG)-> kegg_path
#>
#> Path 2:
#> ec -(KEGG)-> kegg_rxn -(KEGG)-> rclass -(KEGG)-> kegg_path
#>
#> Path 3:
#> ec -(KEGG)-> kegg_glycan -(KEGG)-> kegg_rxn -(KEGG)-> kegg_path
ec2path <- weaveComplex(
graph,
ec ~ kegg_path,
include = "kegg_rxn",
threshold = 0.5
)
#> ec -(KEGG)-> kegg_rxn
#> kegg_rxn -(KEGG)-> kegg_path
#> Warning: names for 6 kegg_path ids not found.
head(ec2path)
#> ec kegg_path cov kegg_path.name
#> 1 1.14.11.21 map00331 0.5000000 Clavulanic acid biosynthesis
#> 2 1.14.11.21 rn00331 0.5000000 <NA>
#> 3 2.1.1.6 map00965 0.5000000 Betalain biosynthesis
#> 4 2.1.1.6 rn00965 0.5000000 <NA>
#> 5 2.3.1.235 map01056 0.6666667 Biosynthesis of type II polyketide backbone
#> 6 2.3.1.235 rn01056 0.6666667 <NA>
searchPath(graph, uniref90 ~ metacyc_path, k = 3)
#> Path 1:
#> uniref90 -(UniProt)-> ec -(WoL)-> metacyc_rxn -(WoL)-> metacyc_path
#>
#> Path 2:
#> uniref90 -(WoL)-> go -(GO)-> metacyc_rxn -(WoL)-> metacyc_path
#>
#> Path 3:
#> uniref90 -(ChocoPhlAn)-> go -(GO)-> metacyc_rxn -(WoL)-> metacyc_path
uniref2path <- weaveComplex(graph, ec ~ metacyc_path)
#> ec -(WoL)-> metacyc_rxn
#> metacyc_rxn -(WoL)-> metacyc_path
head(uniref2path)
#> ec metacyc_path cov
#> 1 |1.1.1.co| PWY-5789 0.06666667
#> 2 |1.1.1.co| PWY-6473 0.33333333
#> 3 |1.1.1.co| PWY-7854 0.11111111
#> 4 |1.1.1.eb| PWY-7882 0.33333333
#> 5 |1.1.1.et| PWY-5516 1.00000000
#> 6 |1.14.14.eo| PWY-5271 1.00000000
#> metacyc_path.name
#> 1 3-hydroxypropanoate/4-hydroxybutanate cycle
#> 2 4-aminobutanoate degradation IV
#> 3 crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)
#> 4 IM-2 type γ-butyrolactones biosynthesis
#> 5 D-xylose degradation II
#> 6 abscisic acid degradation to phaseic acidR session information:
#> R version 4.6.0 (2026-04-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.4 LTS
#>
#> Matrix products: default
#> BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
#>
#> locale:
#> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
#> [9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#>
#> time zone: UTC
#> tzcode source: system (glibc)
#>
#> attached base packages:
#> [1] stats4 stats graphics grDevices utils datasets methods base
#>
#> other attached packages:
#> [1] miaViz_1.21.0 ggraph_2.2.2 ggplot2_4.0.3
#> [4] mia_1.19.8 TreeSummarizedExperiment_2.21.0 Biostrings_2.81.1
#> [7] XVector_0.53.0 SingleCellExperiment_1.35.0 MultiAssayExperiment_1.39.0
#> [10] SummarizedExperiment_1.43.0 Biobase_2.73.1 GenomicRanges_1.65.0
#> [13] Seqinfo_1.3.0 IRanges_2.47.0 S4Vectors_0.51.1
#> [16] BiocGenerics_0.59.0 generics_0.1.4 MatrixGenerics_1.25.0
#> [19] matrixStats_1.5.0 ariadne_0.2.3 BiocStyle_2.41.0
#>
#> loaded via a namespace (and not attached):
#> [1] splines_4.6.0 MultiFactor_0.1.2 ggplotify_0.1.3 filelock_1.0.3
#> [5] tibble_3.3.1 polyclip_1.10-7 XML_3.99-0.23 DirichletMultinomial_1.55.0
#> [9] lifecycle_1.0.5 httr2_1.2.2 vroom_1.7.1 lattice_0.22-9
#> [13] MASS_7.3-65 SnowballC_0.7.1 magrittr_2.0.5 sass_0.4.10
#> [17] rmarkdown_2.31 jquerylib_0.1.4 yaml_2.3.12 otel_0.2.0
#> [21] DBI_1.3.0 RColorBrewer_1.1-3 abind_1.4-8 purrr_1.2.2
#> [25] yulab.utils_0.2.4 tweenr_2.0.3 rappdirs_0.3.4 gdtools_0.5.0
#> [29] ggrepel_0.9.8 tokenizers_0.3.0 irlba_2.3.7 tidytree_0.4.7
#> [33] rentrez_1.2.4 vegan_2.7-3 pkgdown_2.2.0 permute_0.9-10
#> [37] DelayedMatrixStats_1.35.0 codetools_0.2-20 DelayedArray_0.39.1 scuttle_1.23.0
#> [41] ggforce_0.5.0 tidyselect_1.2.1 aplot_0.2.9 farver_2.1.2
#> [45] ScaledMatrix_1.21.0 viridis_0.6.5 BiocFileCache_3.3.0 jsonlite_2.0.0
#> [49] BiocNeighbors_2.7.2 decontam_1.33.0 tidygraph_1.3.1 scater_1.41.1
#> [53] systemfonts_1.3.2 tools_4.6.0 ggnewscale_0.5.2 progress_1.2.3
#> [57] treeio_1.37.0 ragg_1.5.2 Rcpp_1.1.1-1.1 glue_1.8.1
#> [61] gridExtra_2.3 SparseArray_1.13.2 xfun_0.57 mgcv_1.9-4
#> [65] dplyr_1.2.1 withr_3.0.2 BiocManager_1.30.27 fastmap_1.2.0
#> [69] bluster_1.23.0 digest_0.6.39 rsvd_1.0.5 R6_2.6.1
#> [73] gridGraphics_0.5-1 textshaping_1.0.5 RSQLite_3.52.0 ecodive_2.2.6
#> [77] tidyr_1.3.2 fontLiberation_0.1.0 data.table_1.18.4 DECIPHER_3.9.0
#> [81] prettyunits_1.2.0 graphlayouts_1.2.3 httr_1.4.8 htmlwidgets_1.6.4
#> [85] S4Arrays_1.13.0 pkgconfig_2.0.3 gtable_0.3.6 blob_1.3.0
#> [89] S7_0.2.2 janeaustenr_1.0.0 htmltools_0.5.9 fontBitstreamVera_0.1.1
#> [93] bookdown_0.46 scales_1.4.0 png_0.1-9 ggfun_0.2.0
#> [97] knitr_1.51 tzdb_0.5.0 reshape2_1.4.5 rncl_0.8.9
#> [101] nlme_3.1-169 curl_7.1.0 cachem_1.1.0 stringr_1.6.0
#> [105] parallel_4.6.0 vipor_0.4.7 arrow_24.0.0 desc_1.4.3
#> [109] pillar_1.11.1 grid_4.6.0 vctrs_0.7.3 BiocSingular_1.29.0
#> [113] dbplyr_2.5.2 beachmat_2.29.0 cluster_2.1.8.2 beeswarm_0.4.0
#> [117] evaluate_1.0.5 readr_2.2.0 cli_3.6.6 compiler_4.6.0
#> [121] rlang_1.2.0 crayon_1.5.3 tidytext_0.4.3 forcats_1.0.1
#> [125] plyr_1.8.9 fs_2.1.0 ggbeeswarm_0.7.3 ggiraph_0.9.6
#> [129] stringi_1.8.7 viridisLite_0.4.3 BiocParallel_1.47.0 assertthat_0.2.1
#> [133] lazyeval_0.2.3 fontquiver_0.2.1 Matrix_1.7-5 hms_1.1.4
#> [137] patchwork_1.3.2 sparseMatrixStats_1.25.0 bit64_4.8.0 KEGGREST_1.53.0
#> [141] igraph_2.3.1 memoise_2.0.1 bslib_0.10.0 rotl_3.1.1
#> [145] ggtree_4.3.0 bit_4.6.0 ape_5.8-1