r-lequin
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r-lequin [2008/01/28 11:38] – heidi | r-lequin [2009/01/17 10:55] (current) – heidi | ||
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====== R-lequin ====== | ====== R-lequin ====== | ||
- | {{matrix_pairwise_fst.png?220}} {{matrix_hapdistance_between-within_pop_and_groups.png? | + | {{pairwisediffmatrix_03-10-08_at_14-09-16.png? |
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- | **R-lequin is an R interface | + | \\ |
+ | **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 | ||
+ | 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 ===== | ===== R code for graphics ===== | ||
- | * {{master_r-lequin.doc}} | + | === Documentations: |
+ | {{master_r-lequin.pdf|}}\\ | ||
+ | {{r-lequin_graphic_description.pdf|}} | ||
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- | * [[general commands]] | + | |
- | | + | === lines: |
* [[mismatch distribution]] | * [[mismatch distribution]] | ||
* [[heterozygosity]] | * [[heterozygosity]] | ||
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* [[Allelic size range]] (lines with different colors) | * [[Allelic size range]] (lines with different colors) | ||
* [[Molecular diversity indexes]] | * [[Molecular diversity indexes]] | ||
- | * matrix: | + | === matrix: |
* [[Fst Matrix]] | * [[Fst Matrix]] | ||
* read data from a HTML file | * read data from a HTML file | ||
* read data from a XML file | * read data from a XML file | ||
* move legend | * move legend | ||
- | * [[haplotype distance]] (line by line input) | + | |
- | * improved: matrix rotated, more labels | + | |
- | * [[haplotype distance between/ | + | * improved: matrix rotated, more labels |
- | * with mixed data from several populations | + | * [[haplotype distance between/ |
+ | * with mixed data from several populations | ||
* [[Tau]] | * [[Tau]] | ||
* multiple plots in one graphic: | * multiple plots in one graphic: | ||
* [[haplotype distance between/ | * [[haplotype distance between/ | ||
* [[Population average pairwise difference]] | * [[Population average pairwise difference]] | ||
- | * bar: | + | === bar: === |
* [[Allelic size range]] | * [[Allelic size range]] | ||
* [[relative Fis per locus]] | * [[relative Fis per locus]] | ||
* [[expected/ | * [[expected/ | ||
- | * points: | + | === points: |
* [[Population assignment test]] | * [[Population assignment test]] | ||
- | * XML: | + | === XML: === |
* [[read data between XML tags]] | * [[read data between XML tags]] | ||
+ | * [[half matrix]] data | ||
+ | * [[full matrix]] data | ||
+ | * [[table]] data | ||
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+ | |||
===== Arlequin output file changes (HTML to XML) ===== | ===== Arlequin output file changes (HTML to XML) ===== | ||
- | **Delete:** | + | === Delete: |
* < | * < | ||
- | * the space (& | + | * the space (& |
\\ | \\ | ||
- | **Insert:** | + | === Insert: |
* XML declaration on top of the output file: < | * XML declaration on top of the output file: < | ||
<?xml version=" | <?xml version=" | ||
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\\ | \\ | ||
- | **example:** | + | |
+ | |||
+ | \\ | ||
+ | === example: | ||
* {{html_-_bsp_arlequinfile.doc|Arlequinfile HTML}} | * {{html_-_bsp_arlequinfile.doc|Arlequinfile HTML}} | ||
* {{xml_-_bsp_arlequinfile.doc|Arlequinfile XML}} | * {{xml_-_bsp_arlequinfile.doc|Arlequinfile XML}} | ||
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===== tutorials ===== | ===== tutorials ===== | ||
* {{r_tutorial.pdf|small introduction to R}} | * {{r_tutorial.pdf|small introduction to R}} | ||
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* [[http:// | * [[http:// | ||
\\ | \\ | ||
- | * [[xml_presentation|xml presentation]] | + | * [[xml_presentation|XML]] |
r-lequin.1201516718.txt.gz · Last modified: 2008/07/22 13:30 (external edit)