rabhit (version 0.2.5)

hapDendo: 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
)

Value

A multitple samples visualization of the distances between haplotypes.

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.

Examples

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