phyloCNR: Calculating cell-to-cell distances, heirarchical clustering,...

In SingerLab/gac: Genetic Analysis of Cells

Calculating cell-to-cell distances, heirarchical clustering, and generating a tree class 'phylo'

Description

Calculating cell-to-cell distances, heirarchical clustering, and generating a tree class 'phylo'

Usage

phyloCNR(
  cnr,
  root.cell = NULL,
  dist.method = "bray",
  hclust.method = "ward.D2",
  ...
)

Arguments

cnr	a cnr bundle
root.cell	a cellID to root the three.
dist.method	method for calculating cell-to-cell distance (see vegdist)
hclust.method	method for heirarchical clustering (see hclust)
...	other parameters passed to vegdist

Value

Creates a cell-to-cell distance matrix, runs heirarchical clustering, and converts the 'hclust' object to an 'ape' class 'phylo' object.

• cdb cell to cell Bray-Curtis dissimiarly

• hcdb heirarchical clustering of distance matrix

• phylo ape class 'phylo' object

SingerLab/gac documentation built on Oct. 14, 2022, 4:09 a.m.