phylo_cnr | R Documentation |
Calculating cell-to-cell distances, heirarchical clustering, and generating a tree class 'phylo'
phylo_cnr(
cnr,
root.cell = NULL,
dist.method = "bray",
hclust.method = "ward.D2",
tree.method = "bal",
...
)
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 |
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
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>.
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)
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