gl.plot.network: Represents a distance or dissimilarity matrix as a network

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Represents a distance or dissimilarity matrix as a network

Description

This script takes a distance matrix generated by dist() and represents the relationship among the specimens as a network diagram. In order to use this script, a decision is required on a threshold for relatedness to be represented as link in the network, and on the layout used to create the diagram.

Usage

gl.plot.network(
  D,
  x = NULL,
  method = "fr",
  node.size = 3,
  node.label = FALSE,
  node.label.size = 0.7,
  node.label.color = "black",
  alpha = 0.005,
  title = "Network based on genetic distance",
  verbose = NULL
)

Arguments

D	A distance or dissimilarity matrix generated by dist() or gl.dist() [required].
x	A genlight object from which the D matrix was generated [default NULL].
method	One of "fr", "kk" or "drl" [default "fr"].
node.size	Size of the symbols for the network nodes [default 3].
node.label	TRUE to display node labels [default FALSE].
node.label.size	Size of the node labels [default 0.7].
node.label.color	Color of the text of the node labels [default 'black'].
alpha	Upper threshold to determine which links between nodes to display [default 0.005].
title	Title for the plot [default "Network based on genetic distance"].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Details

The threshold for relatedness to be represented as a link in the network is specified as a quantile. Those relatedness measures above the quantile are plotted as links, those below the quantile are not. Often you are looking for relatedness outliers in comparison with the overall relatedness among individuals, so a very conservative quantile is used (e.g. 0.004), but ultimately, this decision is made as a matter of trial and error. One way to approach this trial and error is to try to achieve a sparse set of links between unrelated 'background' individuals so that the stronger links are preferentially shown.

There are several layouts from which to choose. The most popular are given as options in this script.

• fr – Fruchterman, T.M.J. and Reingold, E.M. (1991). Graph Drawing by Force-directed Placement. Software – Practice and Experience 21:1129-1164.

• kk – Kamada, T. and Kawai, S.: An Algorithm for Drawing General Undirected Graphs. Information Processing Letters 31:7-15, 1989.

• drl – Martin, S., Brown, W.M., Klavans, R., Boyack, K.W., DrL: Distributed Recursive (Graph) Layout. SAND Reports 2936:1-10, 2008.

Colors of node symbols are those of the rainbow.

Value

returns no value (i.e. NULL)

Author(s)

Custodian: Arthur Georges – Post to https://groups.google.com/d/forum/dartr

Examples

if ((requireNamespace("rrBLUP", quietly = TRUE)) & (requireNamespace("gplots", quietly = TRUE))) {
test <- gl.subsample.loci(platypus.gl, n = 100)
test <- gl.keep.ind(test,ind.list = indNames(test)[1:10])
D <- gl.grm(test, legendx=0.04)
gl.plot.network(D,test)
}

dartR documentation built on June 8, 2023, 6:48 a.m.