snpgdsDrawTree: Draw a dendrogram
In SNPRelate: Parallel Computing Toolset for Genome-Wide Association Studies (GWAS)

Description Usage Arguments Details Value Author(s) See Also

To draw a dendrogram or the distribution of Z scores

snpgdsDrawTree(obj, clust.count=NULL, dend.idx=NULL,
	type=c("dendrogram", "z-score"), yaxis.height=TRUE, yaxis.kinship=TRUE,
	y.kinship.baseline=NaN, y.label.kinship=FALSE, outlier.n=NULL,
	shadow.col=c(rgb(0.5, 0.5, 0.5, 0.25), rgb(0.5, 0.5, 0.5, 0.05)),
	outlier.col=rgb(1, 0.50, 0.50, 0.5), leaflab="none",
	labels=NULL, y.label=0.2, ...)

`obj`	an object returned by `snpgdsCutTree`
`clust.count`	the counts for clusters, drawing shadows
`dend.idx`	the index of sub tree, plot obj$dendrogram[[dend.idx]], or NULL for the whole tree
`type`	"dendrogram", draw a dendrogram; or "z-score", draw the distribution of Z score
`yaxis.height`	if TRUE, draw the left Y axis: height of tree
`yaxis.kinship`	if TRUE, draw the right Y axis: kinship coefficient
`y.kinship.baseline`	the baseline value of kinship; if NaN, it is the height of the first split from top in a dendrogram; only works when `yaxis.kinship = TRUE`
`y.label.kinship`	if TRUE, show 'PO/FS' etc on the right axis
`outlier.n`	the cluster with size less than or equal to `outlier.n` is considered as outliers; if `NULL`, let `outlier.n = obj$outlier.n`
`shadow.col`	two colors for shadow
`outlier.col`	the colors for outliers
`leaflab`	a string specifying how leaves are labeled. The default `"perpendicular"` write text vertically (by default). `"textlike"` writes text horizontally (in a rectangle), and `"none"` suppresses leaf labels.
`labels`	the legend for different regions
`y.label`	y positions of labels
`...`	Arguments to be passed to the method `"plot(, ...)"`, such as graphical parameters.