phyloDDRC | R Documentation |
Calculating clone-to-clone distances, and estimating a phylogenetic tree
phyloDDRC( cnr, root.clone = NULL, exclude.clones = NULL, dist.method = "bray", hclust.method = "ward.D2", ... )
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) |
hclust.method |
method for heirarchical clustering (see hclust) |
... |
other parameters passed to vegan |
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
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