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how come first PR of multiWGCNA we reverted was about 1.2k lines added and now 117? |
Member
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I am trying to revert to timepoint. Something got lost in wgcna-upd2, perhaps at reverting or at merging. |
Contributor
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ok got it, let us know when its ready to be tested again |
Member
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wait... in wgcna-upd2 17 files changed (many man though). Now I have only 2 files, so I need to check and bring the changes into upd3 correctly. |
Member
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OK I updated upd3 with needed changes from up2. I left out some unrelated changes and will PR seperately from: ai-llm.R (adding tidyprompt), and pgx-plotting.R (some layout changes). |
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- add guard after lasagna.prune_graph that detects 0-vertex result and renders an informative blank plot instead of crashing with "need finite 'xlim' values" - message includes context-aware hints based on the active filters (edge threshold, prune, edge.sign) so the user knows what to adjust - triggered when SP weighting + consensus + high edge threshold collectively zero out all edge weights, leaving no nodes to plot
- cor() returns NaN for constant trait columns, which occurs when
splitting by Condition (each group has only one condition value,
giving zero variance for that trait)
- NaN propagated into the second cor(kme) call used for hclust,
crashing with 'NaN dissimilarity value'
- fix 1: strip all-NaN columns from kme after the first cor(X,Y)
- fix 2: guard the hclust cor() with !is.finite() to catch any
remaining NaN/Inf regardless of origin
- affected plot: consensus WGCNA Dendrograms with Condition split
- lapply over stats[p2] used x[, trait] which crashes when foldChange lacks the selected trait column — happens when splitting by Condition because constant-within-group traits are excluded from foldChange but still present in traitSignificance - replace bare column indexing with safe_col() helper that pads missing columns with NA instead of erroring out - fixes subscript out of bounds in consensus WGCNA Features Table when grouping by Condition
- wgcna.runPreservationWGCNA was calling wgcna.runConsensusWGCNA without summary=FALSE, triggering the AI annotation block added in 6b919d5 which references DEFAULT_LLM before it is defined, crashing with 'object DEFAULT_LLM not found' - preservation WGCNA does not need AI module summaries, so passing summary=FALSE and ai_model=NULL is correct
- safe_col returned a matrix when length(tr)==1, causing do.call(cbind) to name all columns after the trait instead of the p2 stat names (traitSignificance, TSPvalue, foldChange, foldChangePvalue); fix by returning a named vector so list element names are used as col names - wgcna.getConsensusGeneStats now returns NULL early if any layer's wgcna.getGeneStats returns NULL (trait absent from that layer's stats)
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Updates needed for OPG PR bigomics/omicsplayground#1715 (Improvements multiwgcna)
Note: this was previously wgcna-upd2 but something got corrupted in merging. This is a new branch tag.