A high-level wrapper function that executes the entire `ComplexMap` workflow. It takes a list of protein complexes and a gene set matrix (GMT) and performs refinement, enrichment, network construction, and topology calculation.
Usage
createComplexMap(
complexList,
gmt,
similarityMethod = "jaccard",
alpha = 0.75,
ifRefineCpx = FALSE,
layout_seed = 123,
verbose = TRUE,
...
)Arguments
- complexList
A named list where each element is a character vector of protein identifiers representing a complex.
- gmt
A named list where each element is a character vector of genes.
- similarityMethod
The metric used for comparing complexes and functional terms. Defaults to **"jaccard"** to penalize size differences and maintain diversity. Avoid "overlap" if you wish to see specific pathways distinct from generic ones.
- alpha
Numeric (0-1). The weight given to physical protein composition versus functional similarity in the network layout. Defaults to **0.75** (75% physical, 25% functional).
- ifRefineCpx
Logical. If **TRUE**, executes Step 1 to refine the input complex list (merge redundant complexes). If **FALSE**, Step 1 is skipped, and the raw `complexList` is used for downstream analysis. Defaults to **FALSE**.
- layout_seed
Integer seed for reproducible layout. Defaults to 123.
- verbose
A logical value indicating whether to print progress messages.
- ...
Additional arguments passed to core functions: - `minSize`, `maxSize`, `mergeThreshold` (for `refineComplexList` if `ifRefineCpx = TRUE`) - `pAdjustMethod`, `pValueCutoff` (for `runComplexEnrichment`) - `geneSetDb` (for `generateNodeAttributes` semantic clustering)
Details
This function is tuned to generate a **functionally diverse landscape**. It enforces the following logic: 1. **Refinement:** (Optional) Uses Jaccard similarity to merge only highly redundant complexes, preserving biological variants (subsets/supersets). Controlled by `ifRefineCpx`. 2. **Enrichment:** Calculates 'Fold Enrichment' to prioritize specific biological functions over generic ones. 3. **Network:** Builds the layout primarily based on **Physical Composition** (alpha = 0.75), using functional annotations only to group related clusters, not to collapse them.