Constructing pan-genome trees
Creates a pan-genome tree based on a pan-matrix and a distance function.
panTree(pan.matrix, dist.FUN = distManhattan, nboot = 0, linkage = "average", ...)
A valid distance function, see below.
Number of bootstrap samples.
The linkage function, see below.
Additional parameters passed on to the specified distance function, see Details below.
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 (
object) and returns a
dist object. See
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.
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.
Lars Snipen and Kristian Hovde Liland.
Snipen, L., Ussery, D.W. (2010). Standard operating procedure for computing pangenome trees. Standards in Genomic Sciences, 2:135-141.
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# 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")
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