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

View source: R/phyloCNR.R

phyloCNRR Documentation

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.