hapDendo: Hierarchical clustering of haplotypes graphical output

In rabhit: Inference Tool for Antibody Haplotype

Hierarchical clustering of haplotypes graphical output

Description

The hapDendo function generates a graphical output of an hierarchical clustering based on the Jaccard distance between multiple samples' haplotypes.

Usage

hapDendo(
  hap_table,
  chain = c("IGH", "IGK", "IGL", "TRB", "TRA"),
  genes_order = NULL,
  removeIGH = TRUE,
  mark_low_lk = TRUE,
  lk_cutoff = 1
)

Arguments

hap_table	haplotype summary table. See details.
chain	the IG/TR chain: IGH,IGK,IGL,TRB. Default is IGH.
genes_order	A vector of the genes by the desired order. Default is by GENE.loc
removeIGH	if TRUE, 'IGH'\'IGK'\'IGL' prefix is removed from gene names. Default is TRUE.
mark_low_lk	if TRUE, a texture is add for low lK values. Default is TRUE.
lk_cutoff	the lK cutoff value to be considerd low for texture layer. Default is lK<1.

Details

A data.frame created by createFullHaplotype.

Value

A multitple samples visualization of the distances between haplotypes.

Examples

# Plotting haplotype hierarchical clustering based on the Jaccard distance
hapDendo(samplesHaplotype)

rabhit documentation built on Feb. 16, 2023, 9:25 p.m.