phylo_cnr: 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

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

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)
tree.method	minimum evolution phylogenetics method, can be 'bal', 'ols' or NULL. Default is 'bal'.
...	other parameters passed to vegdist

Value

Creates a cell-to-cell distance matrix, runs heirarchical clustering. By defaul cell phylogenetics is infered by fastme.bal, and alternatively by 'fastme.ols'. When 'tree.method = NULL, the 'hclust' object is converted to an 'ape' class 'phylo' object to represent the cell phylogeny.

• cdb cell to cell Bray-Curtis dissimiarly

• hcdb heirarchical clustering of distance matrix

• phylo ape class 'phylo' object

References

Vincent Lefort, Richard Desper, Olivier Gascue. 2015. "FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program". Molecular Biology and Evolution, Volume 32, Issue 10, October 2015, Pages 2798–2800. <https://doi.org/10.1093/molbev/msv150?>

Paradis E, Schliep K (2019). “ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R.” Bioinformatics, *35*, 526-528. <https://doi.org/10.1093/bioinformatics/bty633>.

Oksanen J, Simpson G, Blanchet F, Kindt R, Legendre P, Minchin P, O'Hara R, Solymos P, Stevens M, Szoecs E, Wagner H, Barbour M, Bedward M, Bolker B, Borcard D, Carvalho G, Chirico M, De Caceres M, Durand S, Evangelista H, FitzJohn R, Friendly M, Furneaux B, Hannigan G, Hill M, Lahti L, McGlinn D, Ouellette M, Ribeiro Cunha E, Smith T, Stier A, Ter Braak C, Weedon J (2022). _vegan: Community Ecology Package_. R package version 2.6-4, <https://CRAN.R-project.org/package=vegan>.

Examples

data(cnr)

## unrooted cell phylogenetic tree
cnr <- phylo_cnr(cnr)

cnr$phylo
plot(cnr$phylo)


## rooted cell phylogenetic tree
cnr <- phylo_cnr(cnr, root.cell = "cell0")

cnr$phylo
plot(cnr$phylo)

SingerLab/gac documentation built on March 23, 2024, 5:15 a.m.