feat: persist multi-omics WGCNA at upload via pgx$wgcna_mox slot

.Rbuildignore

@@ -6,3 +6,6 @@
 ^README\.Rmd$
 ^\.github$
 ^LICENSE\.md$
+^\.semquery$
+^\.active_plans$
+^\.agents_context$

NAMESPACE

@@ -107,6 +107,10 @@ export(detectBatchEffects)
 export(detectOutlierSamples)
 export(detect_probetype)
 export(double_center_scale_fast)
+export(drugs.analysisInfo)
+export(drugs.enrichmentTable)
+export(drugs.moaEnrichment)
+export(drugs.supportBucket)
 export(eset.getPhenoData)
 export(eset.parsePhenoFromTitle)
 export(estimateBatchCorrectionVectors)
@@ -388,7 +392,6 @@ export(pgx.createSignatureDatabaseH5)
 export(pgx.createSignatureDatabaseH5.fromMatrix)
 export(pgx.createSingleCellPGX)
 export(pgx.createVipGeneLayer)
-export(pgx.create_reports)
 export(pgx.crosscheckINPUT)
 export(pgx.deconvolution)
 export(pgx.dimPlot)
@@ -434,11 +437,14 @@ export(pgx.getPCSFcentrality)
 export(pgx.getSigGO)
 export(pgx.getSymbolFromFeatureData)
 export(pgx.getTopDrugs)
+export(pgx.getTopGS)
 export(pgx.getTopGeneSets)
 export(pgx.getTopGenes)
+export(pgx.getTopMOA)
 export(pgx.inferCellCyclePhase)
 export(pgx.inferCellType)
 export(pgx.inferGender)
+export(pgx.info)
 export(pgx.initialize)
 export(pgx.justSeuratObject)
 export(pgx.load)
@@ -489,6 +495,8 @@ export(pgx.testPhenoCorrelation)
 export(pgx.testPhenoCorrelation2)
 export(pgx.testTCGAsurvival)
 export(pgx.update_drugs_results)
+export(pgx.update_infographics)
+export(pgx.update_reports)
 export(pgx.variableImportance)
 export(pgx.violinPlot)
 export(pgx.wgcna)
@@ -558,9 +566,9 @@ export(rownames.data.table)
 export(rowscale)
 export(rowsduplicated.dgCMatrix)
 export(rpt.compile_cmap_report)
-export(rpt.compile_sections)
 export(rpt.compile_wgcna_report)
 export(rpt.create_full_report)
+export(rpt.create_summary_report)
 export(run.GSEA)
 export(run.GSEA.LeadingEdge)
 export(run.GSEA.preranked)
@@ -633,6 +641,7 @@ export(wgcna.create_infographic)
 export(wgcna.create_module_infographic)
 export(wgcna.create_report)
 export(wgcna.describeModules)
+export(wgcna.ensureStats)
 export(wgcna.filterColors)
 export(wgcna.getConsensusGeneStats)
 export(wgcna.getConsensusTopGenesAndSets)
@@ -641,6 +650,7 @@ export(wgcna.getModuleCrossGenes)
 export(wgcna.getMultiTopGenesAndSets)
 export(wgcna.getTopGenesAndSets)
 export(wgcna.getTopModules)
+export(wgcna.get_modTraits)
 export(wgcna.init)
 export(wgcna.matchColors)
 export(wgcna.pickSoftThreshold)

R/compute2-extra.R

@@ -17,7 +17,7 @@
 #' @export
 compute_extra <- function(pgx, extra = c(
                             "meta.go", "infer", "deconv", "drugs", ## "graph",
-                            "connectivity", "wordcloud", "wgcna", "mofa"
+                            "connectivity", "wordcloud", "wgcna", "wgcna_mox", "mofa"
                           ), sigdb = NULL, pgx.dir = "./data", libx.dir = "./libx",
                           user_input_dir = getwd(),
                           llm_model = NULL, img_model = NULL
@@ -253,6 +253,41 @@ compute_extra <- function(pgx, extra = c(
     timings <- rbind(timings, c("wgcna", tt))
   }
 
+  if ("wgcna_mox" %in% extra && isTRUE(pgx$datatype %in% c("multi-omics", "multiomics"))) {
+    info("[compute_extra] Computing multi-omics WGCNA...")
+    tt <- system.time({
+      tryCatch(
+        {
+          pgx$wgcna_mox <- wgcna.compute_multiomics(
+            dataX = mofa.split_data(pgx$X),
+            samples = pgx$samples,
+            contrasts = pgx$contrasts,
+            annot = pgx$genes,
+            GMT = pgx$GMT,
+            experiment = pgx$description,
+            power = NULL,
+            ngenes = 2000,
+            deepsplit = 2,
+            minmodsize = 10,
+            minKME = 0.3,
+            compute.enrichment = TRUE,
+            add.gsets = FALSE,
+            add.pheno = FALSE,
+            do.consensus = FALSE,
+            report = FALSE
+          )
+        },
+        error = function(e) {
+          message("[ERROR_WGCNA_MOX] FATAL: ", as.character(e))
+          write(as.character(e), file = paste0(user_input_dir, "/ERROR_WGCNA_MOX"))
+          return(NULL)
+        }
+      )
+    })
+    timings <- rbind(timings, c("wgcna_mox", tt))
+    info("[compute_extra] multi-omics WGCNA done")
+  }
+
   if ("mofa" %in% extra) {
     message(">>> Computing MOFA...")
     tt <- system.time({

R/pgx-annot.R

@@ -1321,6 +1321,10 @@ getHumanOrtholog.biomart <- function(organism, symbols, verbose = 1) {
 #' @export
 probe2symbol <- function(probes, annot_table, query = "symbol",
                          key = NULL, fill_na = FALSE, add_datatype = FALSE) {
+
+  # NULL annot_table: no mapping possible — return probes as-is (same behaviour as fill_na=TRUE)
+  if (is.null(annot_table)) return(probes)
+
   # Prepare inputs. add extra matching columns.
   annot_table <- cbind(rownames = rownames(annot_table), annot_table)
   id.cols <- intersect(c("feature", "gene_name", "symbol"), colnames(annot_table))