====== 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}} \\ \\ **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. ** \\ ===== 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: === * [[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 \\ ===== Arlequin output file changes (HTML to XML) ===== === Delete: === * , ,