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R-lequin

R-lequin is an R interface for the graphical display of Arlequin outputs. It should add value and help interpreting results from large Arlequin analyses.

R code for graphics

Documentations:

master_r-lequin.pdf
r-lequin_graphic_description.pdf

general commands

lines:

mismatch distribution
heterozygosity
Haplotype:
- expected/observed haplotype (with CI)
  - save graphic as a .png file
- Haplotype frequencies in population
Allelic size range (lines with different colors)
Molecular diversity indexes

matrix:

Fst Matrix
- read data from a HTML file
- read data from a XML file
- move legend
haplotype distance:
- haplotype distance (line by line input)
  - improved: matrix rotated, more labels
- haplotype distance between/within two populations
  - with mixed data from several populations
Tau
multiple plots in one graphic:
- haplotype distance between/within populations and groups
- Population average pairwise difference

bar:

points:

Population assignment test

XML:

read data between XML tags
- half matrix data
- full matrix data
- table data

Arlequin output file changes (HTML to XML)

Delete:

<html>, <head>, <style>, <body> and <PRE> tags
the space ( ) in the empty <A> tag or replace it with the space code: &#xAO;

Insert:

XML declaration on top of the output file:

<?xml version="1.0" encoding="ISO-8859-1"?>
<?xml-stylesheet type="text/xsl" href="..."?>

root tag
tags around titles and other text which should be specially formatted
tags around data (respectively around data which should be displayed with no special format)
specific tags around data which is needed to make graphics in R:
- unique names for a special kind of data (the format of the data within this tag must always be the same)

no sample names/population names with wihte space, use '_' instead

example:

tutorials

small introduction to R

links

XML

Masterarbeit, Heidi Lischer

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