R: Genetic transitive graphs

gengraph {adegenet} | R Documentation

## Genetic transitive graphs

### Description

These functions are under development. Please email the author before using them for published work.

The function `gengraph` generates graphs based on genetic distances, so that pairs of entities (individuals or populations) are connected if and only if they are distant by less than a given threshold distance. Graph algorithms and classes from the `igraph` package are used.

`gengraph` is a generic function with methods for the following types of objects:
- `matrix` (only numeric data)
- `dist`
- `genind` objects (genetic markers, individuals)
- `genpop` objects (genetic markers, populations)
- `DNAbin` objects (DNA sequences)

### Usage

    gengraph(x, ...)

    ## S3 method for class 'matrix'
    gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
               plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
               nbreaks=10, ...)

    ## S3 method for class 'dist'
    gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
               plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
               nbreaks=10, ...)

    ## S3 method for class 'genind'
    gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
               plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
               nbreaks=10, ...)

    ## S3 method for class 'genpop'
    gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
               plot=TRUE, show.graph=TRUE, col.pal=funky, method=1,
               truenames=TRUE, nbreaks=10, ...)

    ## S3 method for class 'DNAbin'
    gengraph(x, cutoff=NULL, ngrp=NULL, computeAll=FALSE,
               plot=TRUE, show.graph=TRUE, col.pal=funky, truenames=TRUE,
               nbreaks=10, ...)

### Arguments

`x` | a `matrix`, `dist`, `genind`, `genpop`, or `DNAbin` object. For `matrix` and `dist`, the object represents pairwise (by default, Hamming) distances between considered individuals.
`cutoff` | a `numeric` value indicating the cutoff point, i.e. the distance at which two entities are no longer connected in the garph produced by the method.
`ngrp` | an `integer` indicating the number of groups to be looked for. A message is issued if this exact number could not be found.
`computeAll` | a `logical` stating whether to investigate solutions for every (integer) cutoff point; defaults to FALSE.
`plot` | a `logical` indicating whether plots should be drawn; defaults to TRUE; this operation can take time for large, highly-connected graphs.
`show.graph` | a `logical` indicating whether the found graph should be drawn, only used in the interactive mode; this operation can take time for large, highly-connected graphs; defaults to FALSE.
`col.pal` | a color palette used to define group colors.
`method` | an `integer` ranging from 1 to 6 indicating the type of method to be used to derive a matrix of pairwise distances between populations; values from 1 to 5 are passed to the function `dist.genpop`; other values are not supported.
`truenames` | a logical indicating whether original labels should be used for plotting (TRUE), as opposed to indices of sequences (FALSE).
`nbreaks` | an integer indicating the number of breaks used by the heuristic when seeking an exact number of groups.
`...` | further arguments to be used by other functions; currently not used.

### Value

The class `gengraph` is a list with the following components:

`graph` | a graph of class `igraph`.
`clust` | a list containing group information: `$membership`: an integer giving group membership; `$csize`: the size of each cluster; `$no`: the number of clusters
`cutoff` | the value used as a cutoff point
`col` | the color used to plot each group.

### Author(s)

Original idea by Anne Cori and Christophe Fraser. Implementation by Thibaut Jombart t.jombart@imperial.ac.uk.

### See Also

The `igraph` package.

### Examples

    if(require(ape)){
        data(woodmouse)
        g <- gengraph(woodmouse, cutoff=5)
        g
        plot(g$graph)

    }

[Package adegenet version 2.1.4 Index]