adegenet: gengraph – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

adegenet

gengraph

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.

Examples

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

}

adegenet

Exploratory Analysis of Genetic and Genomic Data

v2.1.3

GPL (>= 2)

Authors

Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>), Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>), Caitlin Collins [ctb], Roman Lustrik [ctb], Marie-Pauline Beugin [ctb], Brian J. Knaus [ctb], Peter Solymos [ctb], Vladimir Mikryukov [ctb], Klaus Schliep [ctb], Tiago Maié [ctb], Libor Morkovsky [ctb], Ismail Ahmed [ctb], Anne Cori [ctb], Federico Calboli [ctb], RJ Ewing [ctb], Frédéric Michaud [ctb], Rebecca DeCamp [ctb], Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)

Initial release

gengraph

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

adegenet

We don't support your browser anymore