commplot: Plot a community or traits on a phylogenetic tree

In DomBennett/MoreTreeTools: Tools for manipulating phylogenetic trees

Description

Plot community or trait data on phylogeny to visualise differences in structure between traits or sites. Use colours to distinguish groups and alpha to distinguish abundances (works like rainbow())

Usage

commplot(cmatrix, tree, groups = rep(1, nrow(cmatrix)), no.margin = TRUE,
  ...)

Arguments

cmatrix	community/trait data matrix (cols taxa, rows sites)
tree	phylogenetic tree (ape class)
groups	trait or site groups

Details

No details

References

No references yet! https://github.com/DomBennett/MoreTreeTools.

Examples

# Generate a balanced tree
tree <- compute.brlen (stree (16, 'balanced'))
# Generate random community data, 2 of 3 different communities
cmatrix <- matrix (round (runif (16*6, 0, 2)), nrow = 6, byrow = TRUE)
colnames (cmatrix) <- tree$tip.label
rownames (cmatrix) <- paste0 ('site_', 1:6)
# Plot community, specify group identitiy of each of the 6 sites
commplot (cmatrix, tree, groups = c (1,1,2,2,3,3))

DomBennett/MoreTreeTools documentation built on May 6, 2019, 2:51 p.m.