| ReadDendrogram {DECIPHER} | R Documentation |
Reads a dendrogram object from a file in Newick (also known as New Hampshire) parenthetic format.
ReadDendrogram(file,
convertBlanks = TRUE,
internalLabels = TRUE,
keepRoot = TRUE)
file |
a connection object or a character string. |
convertBlanks |
Logical specifying whether to convert underscores in unquoted leaf labels to spaces. |
internalLabels |
Logical indicating whether to keep internal node labels as “edgetext” preceding the node in the |
keepRoot |
Logical specifying whether to keep the root node (if one is present) as a dendrogram leaf. |
ReadDendrogram will create a dendrogram object from a Newick formatted tree. Note that all edge lengths must be specified, but labels are optional.
An object of class dendrogram.
Erik Wright eswright@pitt.edu
tf <- tempfile()
dists <- matrix(c(0, 10, 20, 10, 0, 5, 20, 5, 0),
nrow=3,
dimnames=list(c("dog", "elephant", "horse")))
dend1 <- IdClusters(dists, method="NJ", type="dendrogram")
WriteDendrogram(dend1, file=tf)
dend2 <- ReadDendrogram(tf)
layout(matrix(1:2))
plot(dend1, main="Dendrogram Written")
plot(dend2, main="Dendrogram Read")
# Note that the ordering information is lost
any(unlist(dend1) != unlist(dend2)) # TRUE
unlink(tf)