Version Compatibility

Reference examples tested with: SNFtool 2.3+, igraph 2.0+, pheatmap 1.0+.

Before using code patterns, verify installed versions match. If versions differ:

• R: packageVersion('SNFtool') then ?function_name to verify parameters

If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying.

SNFtool argument names are easy to misread: affinityMatrix's width argument is sigma (not alpha or mu), dist2 returns SQUARED Euclidean distance (take the square root), and spectralClustering's K is the number of CLUSTERS, a name collision with the K-neighbors argument of affinityMatrix/SNF.

Similarity Network Fusion

"Stratify my patients using multi-omics data" -> Fuse per-omic patient-similarity networks into one graph and spectral-cluster it - because the clustering always returns the number of subtypes requested, so the subtype is a claim to defend, not a discovery.

• R: SNF() to fuse networks, spectralClustering() to partition, then validate

Scope: patient-similarity-space integration - per-omic affinity networks, SNF fusion, spectral clustering into candidate subtypes, cluster-number choice, and the stability/survival/replication defense, plus the integrative-clustering landscape (NEMO, PINS, iCluster, CIMLR, intNMF, consensus). Feature-space latent factors -> mofa-integration. Supervised feature signatures -> mixomics-analysis. Survival mechanics -> clinical-biostatistics/survival-analysis. Single-cell graph clustering -> single-cell/clustering.