Pantree objects
Pantree object.
"plot"(x, leaf.lab=NULL, col="black", xlab="", main="", cex=1, show.boot=TRUE, ...)
"summary"(object, ...)
"str"(object, ...)Pantree object, see below.Pantree object, see below.Pantree object is created by panTree and contains information to display a pan-genome tree. The plot.Pantree function will display the tree as a dendrogram object.
The argument leaf.lab can be used to give alternative labels, the GID-tags are used by default. leaf.lab must be a vector of labels, one for each genome in the Pantree. The labels may be in any order, but the vector must be named by the GID-tags, i.e. each element in leaf.lab must have a name which is a valid GID-tag for some genome. This is necessary to ensure the alternative labels are placed correctly in the tree.
The argument col specifies the color(s) of the leaf labels in the tree. It can either be a single color or a vector of colors, one for each leaf label (genome). Again, the colors may be in any order, but the vector must be named by the GID-tags, i.e. each element in col must have a name which is a valid GID-tag for some genome.
The argument cex scales the leaf label font size.
The argument show.boot can be used to turn off the display of bootstrap values. Note that if the tree was constructed without bootstrapping, no bootstrap values are available, and this argument has no effect.
Any additional arguments are passed on to the plot.dendrogram function.
Both summary.Pantree and str.Pantree prints a short text describing the Pantree object.
panTree
# See examples in the Help-file for panTree.
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