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. Leaves will be numbered by their labels in alphabetical order.
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") unlink(tf)