DENDRO.cluster: DENDRO specific cluster method on genetic divergence matrix

In zhouzilu/DENDRO: Dna based EvolutioNary tree preDiction by scRna-seq technOlogy

Description

Cluster cells based on the genetic divergence matrix using hierachical cluster methods.

Usage

DENDRO.cluster(dist, method = "ward.D", plot = TRUE, label = NULL, ...)

Arguments

dist	A dissimilarity structure as produced by 'dist'
method	Submethod for 'hclust'. Default is "ward.D", because statistical integreity
plot	TRUE or FALSE, decide whether to plot the result. Default value is TRUE.
label	An integer 1D vector that decide the label color. Default NULL, where no color label.
...	Other arugments can be inherited from plot.phylo in "ape". For example type='fan' for circle cluster plot.

Value

An object of class hclust which describes the tree produced by the clustering process. Check https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/hclust for more detail.

If 'plot==TRUE', a hclust plot will also be displayed.

Author(s)

Zilu Zhou

References

https://www.rdocumentation.org/packages/stats/versions/3.5.1/topics/hclust

Examples

data("DENDRO_demo")
demo_qc = FilterCellMutation(demo$X,demo$N,demo$Z,demo$Info,demo$label)
dist = DENDRO.dist(demo_qc$X,demo_qc$N,demo_qc$Z,show.progress=FALSE)
cluster=DENDRO.cluster(dist,label=demo_qc$label)

zhouzilu/DENDRO documentation built on May 21, 2020, 8 p.m.