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

Description Usage Arguments Value

View source: R/phyloCNR.R

Description

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

Usage

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

Arguments

cnr

a cnr bundle

dist.method

method for calculating cell-to-cell distance (see vegan::vegdist)

hclust.method

method for heirarchical clustering (see hclust)

root.cell

a cellID to root the three.

...

other parameters

Value

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


SingerLab/gac documentation built on Aug. 14, 2021, 10:57 a.m.