graph_plot_compar

The function enables to compare two spatial graphs by
plotting them highlighting the topological similarities and differences
between them. Both graphs should share the same nodes and cannot
be directed graphs.

Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs,	compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://igraph.org/>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.

Paul Savary

graph4lg

Build Graphs for Landscape Genetics Analysis

Gilles Vuidel

Tyler Rudolph

Alexandrine Daniel

graph_plot_compar function

<dl><dt>x</dt>
<dd>A graph object of class <code>igraph</code>.
Its nodes must have the same names as in graph <code>y</code>.</dd>
<dt>y</dt>
<dd>A graph object of class <code>igraph</code>.
Its nodes must have the same names as in graph <code>x</code>.</dd>
<dt>crds</dt>
<dd>A <code>data.frame</code> with the spatial
coordinates of the graph nodes (both <code>x</code> and <code>y</code>).
It must have three columns:<ul>
<li>ID: Name of the graph nodes (character string).
The names must be the same as the node names of the graphs of
class <code>igraph</code> (<code>igraph::V(graph)$name</code>)</li>
<li>x: Longitude of the graph nodes (numeric or integer).</li>
<li>y: Latitude of the graph nodes (numeric or integer).</li>
</ul></dd></dl>

Arguments

Author

Visualize the topological differences between two spatial graphs on a map — graph_plot_compar

<dl>

<dt>x</dt>
<dd>A graph object of class <code>igraph</code>.
Its nodes must have the same names as in graph <code>y</code>.</dd>


<dt>y</dt>
<dd>A graph object of class <code>igraph</code>.
Its nodes must have the same names as in graph <code>x</code>.</dd>


<dt>crds</dt>
<dd>A <code>data.frame</code> with the spatial
coordinates of the graph nodes (both <code>x</code> and <code>y</code>).
It must have three columns:<ul>
<li>ID: Name of the graph nodes (character string).
The names must be the same as the node names of the graphs of
class <code>igraph</code> (<code>igraph::V(graph)$name</code>)</li>
<li>x: Longitude of the graph nodes (numeric or integer).</li>
<li>y: Latitude of the graph nodes (numeric or integer).</li>
</ul></dd>

</dl>

graph_plot_compar: Visualize the topological differences between two spatial graphs on a map

Description

Usage

Value

Arguments

Author

Details

Examples