Masterarbeit, Heidi Lischer

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====== R-lequin ======
{{pairwisediffmatrix_03-10-08_at_14-09-16.png?220}}  {{micdiplhapdistmatrix_withinbetweencompleteexpanded2_03-10-08_at_15-41-55.png?220}} {{sumallelicsizerange_18-11-08_at_13-25-55.png?220}} 
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**R-lequin is a collection of R functions to parse a XML output file of ARLEQUIN version 3.12. R-lequin extracts data and produces graphics. R is an ideal programming language for parsing XML files and for graphic creation because it provides a lot of graphical  techniques and a XML package containing tools for parsing and generating XML within R. The graphics should help to get an impression and to interpret the results produced by ARLEQUIN.\\
R-lequin is a tool to enhance the user friendliness and the readability of the ARLEQUIN output.
**
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===== R code for graphics =====
=== Documentations: ===
{{master_r-lequin.pdf|}}\\
{{r-lequin_graphic_description.pdf|}}

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  * **[[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: ===
    * [[Allelic size range]]
    * [[relative Fis per locus]]
    * [[expected/observed haplotype]] (with CI)
=== points: ===
    * [[Population assignment test]]  
=== XML: ===
    * [[read data between XML tags]]
      * [[half matrix]] data
      * [[full matrix]] data
      * [[table]] data
  

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===== Arlequin output file changes (HTML to XML) =====
=== Delete: ===
  * <html>, <head>, <style>, <body> and <PRE> tags
  * the space (&nbsp;) in the empty <A> tag or replace it with the space code: &#xAO;

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=== Insert: ===
  * XML declaration on top of the output file: <code>
<?xml version="1.0" encoding="ISO-8859-1"?>
<?xml-stylesheet type="text/xsl" href="..."?>
</code>
  * 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)

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

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=== example: ===
   * {{html_-_bsp_arlequinfile.doc|Arlequinfile HTML}}
   * {{xml_-_bsp_arlequinfile.doc|Arlequinfile XML}}
   * {{xslt_-_bsp_arlequinfile.doc|XSLT}}
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===== tutorials =====
  * {{r_tutorial.pdf|small introduction to R}}





===== links =====
  * [[http://www.r-project.org|r-project]]
  * [[http://gbi.agrsci.dk/statistics/courses/phd06/material/Day1-R-Intro/r-graphics.pdf|graph basics]]
  * [[http://addictedtor.free.fr/graphiques/thumbs.php|graph gallery]]
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  * [[xml_presentation|XML]]