phylo_ddrc: Calculating clone-to-clone distances, and estimating a...

In SingerLab/gac: Genetic Analysis of Cells

Calculating clone-to-clone distances, and estimating a phylogenetic tree

Description

Calculating clone-to-clone distances, and estimating a phylogenetic tree

Usage

phylo_ddrc(
  cnr,
  root.clone = NULL,
  exclude.clones = NULL,
  dist.method = "bray",
  tree.method = "bal",
  spr = TRUE,
  ...
)

Arguments

cnr	a cnr bundle
root.clone	a single clone to root the tree
exclude.clones	vector of clones to exclude
dist.method	method for calculating cell-to-cell distance (see vegan::vegdist)
tree.method	method for phylogenetic tree construction either "bal", "ols", or "nj". default is "bal"
spr	parameter specific to fastme.bal. Performs Subtree Pruning and Regrafting. Ignored in all other methods. Default is TRUE
...	other parameters passed to root

Value

Creates a cell-to-cell distance matrix, runs heirarchical clustering. By default a phylogenetic tree is constructed using fastme.bal, alternative algorithms are fastme.ols or nj.

• DDRC.dist clone to clone Bray-Curtis dissimiarly

• DDRC.phylo phylogenetic tree of class 'phylo' from R/ape

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)

cnr <- phylo_cnr(cnr)
cnr <- setBrayClusters(cnr)
cnr <- get_cluster_profiles(cnr, cluster.column = "BrayC")

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

cnr$DDRC.phylo
plot(cnr$DDRC.phylo)


## rooted cell phylogenetic tree
cnr <- phylo_ddrc(cnr, root.clone = "C2")

cnr$DDRC.phylo
plot(cnr$DDRC.phylo)

## change method to ols
cnr <- phylo_ddrc(cnr, root.clone = "C2", tree.method = "ols")

cnr$DDRC.phylo
plot(cnr$DDRC.phylo)

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