Expanding clustering

[ncborcherding]

Per issue #546 - expanded the clustering algorithms by updating buildNetwork() in immApex 1.4.1

• dist_type = c("levenshtein", "hamming", "damerau", "nw", "sw") - default: "levenshtein" (backward compatible)
• normalize = c("none", "length", "maxlen")
  • "none" leaves as raw metric units
  • "length" = distance / sequence_length_of_pair (e.g., min or mean; see norm_ref)
  • "maxlen" = distance / max(nchar(s1), nchar(s2))
• Alignment controls (only used for dist_type %in% c("nw","sw")):
  • dist_mat = c("BLOSUM62", "PAM30", etc)

[ncborcherding]

Will need to get the immApex changes uploaded to bioconductor

[codecov]

Codecov Report

❌ Patch coverage is 96.42857% with 5 lines in your changes missing coverage. Please review.

Files with missing lines	Patch %	Lines
R/utils.R	78.57%	3 Missing ⚠️
R/combineContigs.R	98.13%	2 Missing ⚠️

Files with missing lines	Coverage Δ
R/alluvialClones.R	80.76% <ø> (ø)
R/clonalAbundance.R	78.08% <ø> (ø)
R/clonalCluster.R	90.41% <100.00%> (+1.20%)	⬆️
R/clonalCompare.R	95.06% <ø> (ø)
R/clonalDiversity.R	93.50% <ø> (ø)
R/clonalHomeostasis.R	93.87% <ø> (ø)
R/clonalLength.R	80.00% <ø> (ø)
R/clonalNetwork.R	81.39% <ø> (ø)
R/clonalOverlap.R	96.73% <ø> (ø)
R/clonalProportion.R	93.18% <ø> (ø)
... and 12 more

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