map2dend: Transforming a map into a dendrogram

In pergola: Toolbox for Polyploid Genetic Data

Description

Create dendrogram object. The map specific distance are ignored and only the grouping and ordering is maintained. Allows for comparison of whole map with package 'dendextend'

Usage

map2dend(map, mergeoff = 0L)

Arguments

map	One map. Required.
mergeoff	Numeric, offset between chromosomes, to avoid equal heights in dendrogram. Equal heights lead to problems in cor_bakers_gamma().

Value

Dendogram object.

Examples

data(simTetra)
simTetrageno <- bases2genotypes(simTetra, 4)
rfMat <- calcRec(simTetrageno, 4)
split <- splitChr(rfMat, nchr = 7)
split <- sortLeafs(rfMat, split)
map <- pullMap(rfMat, split = split)   
dend <- map2dend(map)  
plot(dend)

pergola documentation built on May 2, 2019, 3:22 a.m.