pergola (version 1.0)

maketangle: Create a gray scale tanglegram

Description

Create tanglegram. Removes markers, that are not in both trees. Calculates alternating light and dark shades of grey.

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.

Examples

data(simTetra)
simTetraGen <- bases2genotypes(simTetra, 4)
rfMat <- calcRec(simTetraGen, 4)
split <- splitChr(rfMat, nchr = 7)
split <- sortLeafs(rfMat, split)
map <- pullMap(rfMat, split = split)  
dend <- map2dend(map)  
maketangle(dend, dend, cutheight = 500, k = 7, ncol = 7)