micropan (version 1.2)

panTree: Constructing pan-genome trees

Description

Creates a pan-genome tree based on a pan-matrix and a distance function.

Usage

panTree(pan.matrix, dist.FUN = distManhattan, nboot = 0,
  linkage = "average", ...)

Arguments

pan.matrix

A Panmat object, see panMatrix.

dist.FUN

A valid distance function, see below.

nboot

Number of bootstrap samples.

linkage

The linkage function, see below.

…

Additional parameters passed on to the specified distance function, see Details below.

Value

This function returns a Pantree object, which is a small (S3) extension to a list with 4 components. These components are named Htree, Nboot, Nbranch and Dist.FUN.

Htree is a hclust object. This is the actual tree. Nboot is the number of bootstrap samples. Nbranch is a vector listing the number of times each split/clade in the tree was observed in the bootstrap procedure. Dist.FUN is the name of the distance function used to construct the tree.

Details

A pan-genome tree is a graphical display of the genomes in a pan-genome study, based on some pan-matrix (Snipen & Ussery, 2010). panTree is a constructor that computes a Pantree object, use plot.Pantree to actually plot the tree.

The parameter dist.FUN must be a function that takes as input a numerical matrix (Panmat object) and returns a dist object. See distManhattan or distJaccard for examples of such functions. Any additional arguments (...) are passed on to this function.

If you want to have bootstrap-values in the tree, set nboot to some appropriate number (e.g. nboot=100).

The tree is created by hclust (hierarchical clustering) using the average linkage function, which is according to Snipen & Ussery, 2010. You may specify alternatives by the parameter linkage, see hclust for details.

References

Snipen, L., Ussery, D.W. (2010). Standard operating procedure for computing pangenome trees. Standards in Genomic Sciences, 2:135-141.

See Also

panMatrix, distManhattan, distJaccard, plot.Pantree.

Examples

# NOT RUN {
# Loading a Panmat object, constructing a tree and plotting it 
data(list="Mpneumoniae.blast.panmat",package="micropan")
my.tree <- panTree(Mpneumoniae.blast.panmat)
plot(my.tree)

# Computing some weights to be used in the distManhattan
# function below...
w <- geneWeights(Mpneumoniae.blast.panmat,type="shell")
# Creating another tree with scaled and weighted distances and bootstrap values
my.tree <- panTree(Mpneumoniae.blast.panmat, scale=0.1, weights=w)

# ...and plotting with alternative labels and colors from Mpneumoniae.table
data(list="Mpneumoniae.table",package="micropan")
labels <- Mpneumoniae.table$Strain
names(labels) <- Mpneumoniae.table$GID.tag
cols <- Mpneumoniae.table$Color
names(cols) <- Mpneumoniae.table$GID.tag
plot(my.tree, leaf.lab=labels, col=cols,cex=0.8, xlab="Shell-weighted Manhattan distances")

# }