DENDRO.tree: Construct a phylogenetic tree

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

Description

This method constructs a phylogenetic tree with Neighbor Joining method (implemented in 'phangorn'), suggesting the evolutionary relationship between different subclones.

Usage

DENDRO.tree(Z_cluster, label_cluster = NULL)

Arguments

Z_cluster	An mutation indicator matrix (1 for mutation, 0 for normal) across subclones (column) and loci (row).
label_cluster	Cluster labels, which will be used to color phylogenetic tree node. Better to track cells and clusters. This is optional. Default NULL

Value

void. A phylogenetic tree will be plotted.

Author(s)

Zilu Zhou

References

https://cran.r-project.org/web/packages/phangorn/index.html

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$label)
icd = DENDRO.icd(dist,cluster)
DENDRO_label = cutree(cluster,3)
demo_cluster = DENDRO.recalculate(demo_qc$X,demo_qc$N, demo_qc$Info, demo_qc$DENDRO_label, cluster.name=c('Cluster3','Cluster2','Cluster1'))
DENDRO.tree(demo_cluster$Z)

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