hapDendo: Hierarchical clustering of haplotypes graphical output

Description Usage Arguments Details Value Examples

View source: R/graphic_functions.R

Description

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

Usage

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hapDendo(
  hap_table,
  chain = c("IGH", "IGK", "IGL"),
  gene_sort = c("name", "position"),
  removeIGH = TRUE,
  mark_low_lk = TRUE,
  lk_cutoff = 1
)

Arguments

hap_table

haplotype summary table. See details.

chain

the IG chain: IGH,IGK,IGL. Default is IGH.

gene_sort

if by 'name' the genes in the output are ordered lexicographically, if by 'position' only functional genes are used and are ordered by their chromosomal location. Default is 'position'.

removeIGH

if TRUE, 'IGH'\'IGK'\'IGL' prefix is removed from gene names. Defualt is TRUE.

mark_low_lk

if TRUE, a texture is add for low lK values. Defualt is TRUE.

lk_cutoff

the lK cutoff value to be considerd low for texture layer. Defualt is lK<1.

Details

A data.frame created by createFullHaplotype.

Value

A multitple samples visualization of the distances between haplotypes.

Examples

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

rabhit documentation built on July 12, 2020, 1:06 a.m.