Description Usage Arguments Details Examples
The tree object here is ape
tree.
1 2 3 4 | annotateRAXMLTree(tree, taxa.map, anno.tree.file = "annotated-tree.nex",
no.match = "unknown")
renameTips(tree, pattern, replacement, ...)
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tree |
The ape tree object required. | ||||||||||||||||
taxa.map |
The data.frame to map tree tips to traits. It must have at least 2 columns, where the 1st column is tree tip label. For example,
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anno.tree.file |
The file path to load a tree
that can be imported into FigTree including annotations.
If NA, as default, to overwrite the | ||||||||||||||||
pattern, replacement, ... |
Arguments of | ||||||||||||||||
tree.file |
The file path to load a tree generated by RAxML. |
annotateRAXMLTree
annotates a RAxML tree to visualise in FigTree.
renameTips
renames tree tips. It also can be used to insert annotations
using regular expression.
1 2 3 4 5 6 7 8 | tree <- read.tree("RAxML_bestTree.16s.txt")
tree1 <- renameTips(tree, taxa.map, "16s_RAxML.nex")
# remove "_Viridiplantae" postfix from tips
tree2 <- renameTips(tree, "_Viridiplantae", "")
# AB1_Soil.123_Metazoa:0.016 => AB1_Soil.123_Metazoa[&taxon=Metazoa]:0.016
tree2 <- renameTips(tree, "([a-zA-Z0-9\\_\\.]+)_([[a-zA-Z]+):", "\\1_\\2[\\&taxon=\\2]:")
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