treeDists {clstutils} | R Documentation

## Provide objects for determining distances among nodes of a reference tree.

### Description

Provides objects (dists, paths) that can be used to calculate vectors of distances between an internal node and each leaf node. Also returns a square matrix of distances between leaf nodes.

### Usage

    treeDists(placefile, distfile)

### Arguments

`placefile` | path to `pplacer` output
`distfile` | path to output of `guppy distmat`

### Details

A placement on an edge looks like this:

     proximal
      |
      |   d_p
      |
      |---- x
      |
      |   d_d
      |
      |
     distal

d_p is the distance from the placement x to the proximal side of the edge, and d_d the distance to the distal side.

If the distance from x to a leaf y is an S-distance Q, then the path from x to y will go through the distal side of the edge and we will need to add d_d to Q to get the distance from x to y. If the distance from x to a leaf y is a P-distance Q, then the path from x to y will go through the proximal side of the edge, and we will need to subtract off d_d from Q to get the distance from x to y. In either case, we always need to add the length of the pendant edge, which is the second column.

To review, say the values of the two leftmost columns are a and b for a given placement x, and that it is on an edge i. We are interested in the distance of x to a leaf y, which is on edge j. We look at the distance matrix, entry (i,j), and say it is an S-distance Q. Then our distance is Q+a+b. If it is a P-distance Q, then the distance is Q-a+b.

The distances between leaves should always be P-distances, and there we need no trickery.

(thanks to Erick Matsen for this description)

### Value

A list with the following elements:

`dists` | rectangular matrix of distances with rows corresponding to all nodes in pplacer order, and columns corresponding to tips in the order of the corresponding `phylo{ape}` object.
`paths` | rectangular matrix in the same configuration as `dists` with values of 1 or -1 if the path between nodes is serial or parallel, respectively (see Details)
`dmat` | square matrix containing distances between pairs of tips.

### Note

The output of this function is required for `classifyPlacements`.

### Author(s)

Noah Hoffman

### References

Documentation for `pplacer` and `guppy` can be found here: http://matsen.fhcrc.org/pplacer/

### See Also

`classifyPlacements`

### Examples

    placefile <- system.file('extdata','merged.json', package='clstutils')
    distfile <- system.file('extdata','merged.distmat.bz2', package='clstutils')
    treedists <- treeDists(placefile, distfile)

    ## coordinates of a single placement
    placetab <- data.frame(at=49, edge=5.14909e-07, branch=5.14909e-07)

    ## dvects is a matrix in which each row corresponds to a vector of
    ## distances between a single placement along the edge of the reference
    ## tree used to generate 'distfile', and each column correspons to a
    ## reference sequence (ie, a terminal node).

    dvects <- with(placetab, {
    treedists$dists[at+1,,drop=FALSE] + treedists$paths[at+1,,drop=FALSE]*edge + branch
    })

[Package clstutils version 1.40.1 Index]