Pantree objectsGeneric functions for Pantree objects.
# S3 method for Pantree
plot(x, leaf.lab = NULL, col = "black", xlab = "",
main = "", cex = 1, show.boot = TRUE, ...)# S3 method for Pantree
summary(object, ...)
A Pantree object, see below.
Alternative labels for the leaves, see below.
Color of the leaf labels, see below.
Text for the x-axis (distance-axis) of the plotted tree.
Title above the plotted tree.
Scaling of the leaf labels of the plotted tree.
Logical to turn off plotting of bootstrap values.
Additional arguments, see below.
A Pantree object, see below.
A 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.
summary.Pantree prints a short text describing
the Pantree object.
# NOT RUN {
# See examples in the Help-file for panTree.
# }
Run the code above in your browser using DataLab