makeTangle: Create a gray scale tanglegram

In grafab/pergola: Toolbox for Polyploid Genetic Data

Description

Create tanglegram. Removes markers, that are not in both trees. Calculates alternating light and dark shades of grey. This function is a wrapper to functions of dendextend

Usage

makeTangle(dend1, dend2, cutheight, k = NULL, ncol = k, ...)

Arguments

dend1	First dendrogram. Required.
dend2	Second dendrogram. Required.
cutheight	The height, at which dend1 is cut. Influences number of colors.
k	Number of desired linkage groups.
ncol	Number of desired colors.
...	Other parameters are forwarded to the tanglegram command.

Value

None. Plotting only.

References

Galili T. (2015), dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering, Bioinformatics

Examples

data(simTetra)
simTetraGen <- basesToGenotypes(simTetra, 4)
rfMat <- calcRec(simTetraGen, 4)
split <- splitChr(rfMat, nchr = 7)
split <- sortLeafs(rfMat, split)
map <- pullMap(rfMat, split = split)
dend <- mapToDend(map)
makeTangle(dend, dend, cutheight = 500, k = 7, ncol = 7)

grafab/pergola documentation built on May 17, 2019, 8:18 a.m.