[ RDocumentation ](/)

Moon  [ ](https://github.com/datacamp/rdocumentation-2.0) [ Learn R
](https://www.datacamp.com/learn/r)

Search all packages and functions

[ micropan  (version  1.0  ) ](/packages/micropan/versions/1.0)

#  plot.Pantree: Plotting and printing ` Pantree ` objects

##  Description

Generic functions for plotting and printing the content of a ` Pantree `
object.

##  Usage

    
    
    "plot"(x, leaf.lab=NULL, col="black", xlab="", main="", cex=1, show.boot=TRUE, ...)
    "summary"(object, ...)
    "str"(object, ...)

##  Arguments

x

A ` Pantree ` object, see below.

object

A ` Pantree ` object, see below.

leaf.lab

Alternative labels for the leaves, see below.

col

Color of the leaf labels, see below.

xlab

Text for the x-axis (distance-axis) of the plotted tree.

main

Title above the plotted tree.

cex

Scaling of the leaf labels of the plotted tree.

show.boot

Logical to turn off plotting of bootstrap values.

...

Additional arguments, see below.

##  Details

A ` Pantree ` object is created by ` [ panTree
](/link/panTree?package=micropan&version=1.0) ` and contains information to
display a pan-genome tree. The ` [ plot.Pantree
](/link/plot.Pantree?package=micropan&version=1.0) ` function will display the
tree as a ` [ dendrogram ](/link/dendrogram?package=micropan&version=1.0) `
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
](/link/plot.dendrogram?package=micropan&version=1.0) ` function. Both ` [
summary.Pantree ](/link/summary.Pantree?package=micropan&version=1.0) ` and `
[ str.Pantree ](/link/str.Pantree?package=micropan&version=1.0) ` prints a
short text describing the ` Pantree ` object.

##  See Also

` [ panTree ](/link/panTree?package=micropan&version=1.0) `

##  Examples

[ Run this code
](https://www.datacamp.com/datalab/preview?_tag=rdocs&rdocsPath=packages%2Fmicropan%2Fversions%2F1.0%2Ftopics%2Fplot.Pantree&utm_source=r-docs&utm_medium=docs&utm_term=plot.Pantree&utm_content=run_example_in_datalab)

    
    
    # See examples in the Help-file for panTree.
    

Run the code above in your browser using  [ DataLab
](https://www.datacamp.com/datalab/preview?_tag=rdocs&rdocsPath=packages%2Fmicropan%2Fversions%2F1.0%2Ftopics%2Fplot.Pantree&utm_source=r-docs&utm_medium=docs&utm_term=plot.Pantree&utm_content=run_example_in_datalab)

Powered by  [ DataCamp ](https://www.datacamp.com/)