gengraph | R Documentation |
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)
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, ...)
x |
a |
cutoff |
a |
ngrp |
an |
computeAll |
a |
plot |
a |
show.graph |
a |
col.pal |
a color palette used to define group colors. |
method |
an |
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. |
The class gengraph
is a list with the following
components:
graph |
a graph of class |
clust |
a list containing group information: |
cutoff |
the value used as a cutoff point |
col |
the color used to plot each group. |
Original idea by Anne Cori and Christophe Fraser. Implementation by Thibaut Jombart t.jombart@imperial.ac.uk.
The igraph
package.
if(require(ape)){ data(woodmouse) g <- gengraph(woodmouse, cutoff=5) g plot(g$graph) }
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