Diversity Maps Files

Diversity Maps 0.0.3

REQUIRES:

Perl 5.6.x or higher;
Perl module: Postscript::Simple;
Perl module: Getopt::Long (included in most distributions).

If you don't have these modules, use the Standalone version of Diversity Maps.


USAGE: 

> perl DiversityMaps.pl [options] [input_file output_file]
or
> ./DiversityMaps.pl [options] [input_file output_file]

If input/output is not specified, the program reads file 'infile' from the current directory and writes out 'Ref1-Ref2.ps', where Ref1 and Ref2 are reference accession names.


EXAMPLE:

perl DiversityMaps.pl -r1 Morex -r2 Barke -cmax 26 -fs 8 Barley_OPA.txt BOPA_Morex-Barke.ps


OPTIONS:

-r1 <name>		First reference accession (default: auto-select)
-r2 <name>		Second reference accession (default: auto-select)
-rs <name>		Use a single reference accession (default: off)
-i			Ignore non-informative states (default: on)
-s			Sort accessions by similarity (default: off)
-p			Passport mode (default: off)

-cmax <integer>		Maximum number of chromosomes per page
-cw <value>		Chromosome width (default: 1.4, or 18 with -p)
-ch <value>		Chromosome maximum height, mm (default: 200)
-cs <value>		Space between chromosomes, mm (default: 0.22, or 7 with -p)
-lw <value>		Line width, mm (default: 0.02)
-fs <value>		Font size, points (default: 5, or 15 with -p)

-acolor <red,green,blue>	Reference 1 color (default: 255,127,127)
-bcolor <red,green,blue>	Reference 2 color (default: 127,127,255)
-xcolor <red,green,blue>	Non-ref color (default: 240,240,127)
-ncolor <red,green,blue>	Noninformative color (default: 220,220,220)
-acolorh <red,green,blue>	Reference 1 line color (default: 255,63,63)
-bcolorh <red,green,blue>	Reference 2 line color (default: 63,63,255)
-xcolorh <red,green,blue>	Non-ref line color (default: 255,255,63)
-ncolorh <red,green,blue>	Noninformative line color (default: 235,235,235)


INPUT FILE FORMAT:

Chromosome	chr1	chr1	chr1	chr2	chr2	...
Position	0.1	1.9	12.6	2	8.3	...
Accession1	A	B	B	-	B	...
Accession2	B	B	-	A	B	...
...

1st line should contain a word 'Chromosome', followed by arbitrary chromosome names or numbers, separated by spaces or tabulation;
2nd line should contain a word 'Position', followed by marker/SNP positions in cM, bp or other units;
3rd line onwards should contain an accession name and single-letter marker states: 'A', 'B' or '-' (missing data).
Accession names should not contain spaces; the table should be fully populated (add '-' for missing datapoints).

***

CHANGES from 0.0.2:

1. ADDED: Automatic reference selection. 
If no references are specified with -r1/-r2, it selects the pair of accessions with the largest genetic distance from each other (for example, in F2 population the parents will most probably be selected as references).
If only one reference is specified (either -r1 or -r2), the second reference is selected automatically.

2. ADDED: Single reference option.
With -rs <name>, you can choose to work with a single reference only.