Diversity Maps Files

Diversity Maps 0.0.2

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: line #1)
-r2 <name>		Second reference accession (default: line #2)
-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).