plotNetMDS

This function plots a haplotype network using a layout calculated from
 an MDS performed on the pairwise distance matrix. The haplotypes have
 always the same positions for different networks.

hplot

Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, including from VCF files, and for the analysis of population nucleotide sequences and micro-satellites including coalescent analyses, linkage disequilibrium, population structure (Fst, Amova) and equilibrium (HWE), haplotype networks, minimum spanning tree and network, and median-joining networks.

Emmanuel Paradis

pegas

Population and Evolutionary Genetics Analysis System

Thibaut Jombart

Zhian N. Kamvar

Brian Knaus

Klaus Schliep

Alastair Potts

David Winter

plotNetMDS function

<dl> <dt>net</dt>
<dd>an object of class <code>"haploNet"</code>.</dd> <dt>d</dt>
<dd>an object of class <code>"dist"</code> (or a matrix).</dd> <dt>k</dt>
<dd>the number of dimensions of the plot (2 or 3).</dd> <dt>show.mutation</dt>
<dd>a logical value: if <code>TRUE</code>, the number of
 steps is printed on the links.</dd> <dt>col</dt>
<dd>the colours of the links; by default, semi-transparent
 green.</dd> <dt>font</dt>
<dd>the font used to print the labels; bold by default.</dd> <dt>cex</dt>
<dd>the character expansion of the labels.</dd></dl>

Arguments

Author

Plot Networks With MDS Layout — plotNetMDS

<dl>

 <dt>net</dt>
<dd>an object of class <code>"haploNet"</code>.</dd>

 <dt>d</dt>
<dd>an object of class <code>"dist"</code> (or a matrix).</dd>

 <dt>k</dt>
<dd>the number of dimensions of the plot (2 or 3).</dd>

 <dt>show.mutation</dt>
<dd>a logical value: if <code>TRUE</code>, the number of
 steps is printed on the links.</dd>

 <dt>col</dt>
<dd>the colours of the links; by default, semi-transparent
 green.</dd>

 <dt>font</dt>
<dd>the font used to print the labels; bold by default.</dd>

 <dt>cex</dt>
<dd>the character expansion of the labels.</dd>

</dl>

Plot Networks With MDS Layout

plotNetMDS: Plot Networks With MDS Layout

Description

Usage

Value

Arguments

Author

References

See Also

Examples