feat: persist multi-omics WGCNA at upload via pgx$wgcna_mox slot#477
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- move wgcna.get_modTraits, wgcna.getTopGenesAndSets (+ multi/consensus variants), wgcna.describeModules from pgx-wgcna.R to a dedicated pgx-wgcna-report.R module; new wgcna.getTopModules absorbs the prior wrapper and adds a min_modules floor (default 5L) so downstream consumers always get a renderable selection - add wgcna.ensureStats() to lazily populate wgcna\$net\$labels and wgcna\$stats for older PGX files that ship without them; idempotent guard prevents wgcna.getGeneStats errors on example-data and similar - harden probe2symbol with a NULL-guard on annot_table so callers can drop their local resolve_symbols defensive wrappers; behaviour unchanged when annot_table is provided
- new pgx-drugs-report.R exports drugs.analysisInfo, drugs.enrichmentTable, drugs.moaEnrichment, drugs.supportBucket; promoted from omicsplayground board.drugconnectivity so on-the-fly fgsea MOA enrichment and L1000-vs-sensitivity NES direction semantics are reusable across boards and pipelines - lift %||% to utils.R as a backward-compat null-coalesce helper (Depends R >= 3.5 — base R 4.4 operator not yet available)
- some L1000 / CMap drug MOA and target strings carry mixed-encoding bytes (eg the 0xD0 byte in 'serotonin<d0>norepinephrine reuptake inhibitor'); enc2utf8 alone does not strip these, so strsplit's regex engine fails with 'input string is invalid' and 'unable to translate to a wide string' warnings - replace enc2utf8 with iconv(from='UTF-8', to='UTF-8', sub='') which re-parses the input as UTF-8 and silently drops invalid byte sequences; downstream tokenisation only needs the ASCII separators (pipe / semicolon / comma) so dropping the offending bytes does not lose any information that the splitter would have used
- add .semquery (semquery index store), .active_plans (in-progress plan files) and .agents_context (cross-agent scratch notes) to .Rbuildignore so devtools::install / R CMD build no longer complain about non-portable hidden directories inside the package root
- add wgcna_mox branch to compute_extra() gated on
pgx$datatype %in% c('multi-omics','multiomics'); calls
wgcna.compute_multiomics() with the multiwgcna board's parameter
set (deepsplit=2, power=NULL, ngenes=2000, minmodsize=10,
minKME=0.3, compute.enrichment=TRUE) and writes the result to
pgx$wgcna_mox alongside the existing single-omics pgx$wgcna so
both representations coexist (deprecation deferred)
- until now the multi-omics WGCNA only existed as a Shiny reactive
in the webapp's multiwgcna board and was never persisted, so any
downstream consumer (AI reports, copilot context, re-analysis)
saw a NULL wgcna_mox slot on multi-omics PGX files
- new block uses info() rather than message() for non-error
progress lines (matches the convention emerging across compute
pipeline); error reporting keeps the message() + ERROR_WGCNA_MOX
marker-file pattern shared by the other compute_extra branches
phisanti
requested review from
ESCRI11 and
ivokwee
and removed request for
ESCRI11
ESCRI11
approved these changes
May 28, 2026
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Before: multi-omics WGCNA lived only in webapp reactive
r_multiwgcna. Never written topgx. Downstream sawNULLslot. AI reports, Copilot context, and re-analysis are all blind to it.Now, if
wgcna %in% compute_extra, andpgx$datatype %in% c("multi-omics","multiomics")then callwgcna.compute_multiomics()atpgx.Compute().