MAJOR CHANGES:
Leiden Community Detection: Added support for Leiden algorithm as
an alternative to hierarchical clustering. Use
clustering_method = "leiden" in
inferAlleleClusters(). This is particularly useful for D
and J segments with variable-length sequences.
Generalized Distance Functions: The new igDistance()
function supports multiple distance calculation methods:
Multi-locus Support: inferAlleleClusters() now
explicitly supports all V/D/J segments with the locus
parameter.
New Visualization Functions:
plotTruncatedTree(): Publication-quality circular tree
with collapsed subgroupsplotCommunityNetwork(): Network visualization of
cluster relationshipsplotSilhouetteOptimization(): Resolution parameter
optimization plotplotClusterComparison(): Compare hierarchical and
Leiden clustering resultsCLASS SYSTEM CHANGES:
GermlineCluster is now an S3 class
instead of S4.
$ instead of @ (e.g.,
result$alleleClusterTable)print(), summary(), and
plot() S3 methodsclusteringMethod,
communityObject, graphObject,
distanceMatrix, silhouetteScore,
resolutionParameter, locusAPI CHANGES:
ighvDistance() is deprecated in favor of
igDistance() (backward compatible wrapper provided)ighvClust() is deprecated in favor of
igClust() (backward compatible wrapper provided)inferAlleleClusters() has new parameters but maintains
backward compatibilityDEPENDENCIES:
igraph, stringdist,
cluster, apeComplexHeatmap, dplyr,
ggtreedplyr (replaced with
data.table operations)MINOR CHANGES:
Author and
Maintainer fieldstestthat (edition 3)BUG FIXES:
dplyr::between() callsdplyr::bind_rows() callsinferGenotypeAllele
to simplify genotype by asc annotation.genotype_confidence.The confidence is calculated as the Z score of the allele count, repertoire depth, and the allele absolute threshold.
download_zenodo_files.download_zenodo_files.download_zenodo_files.
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