plot.contig.numbers.R

Description

Visualize the file loci_contignumbers.txt as a PDF, taking taxon groups into account.

Usage

plot.contig.numbers.R <file> <file>

Dependencies

Arguments

# Required
1) <file|CHR>:  Path to collected contig numbers (loci_contignumbers.txt).

# Optional [DEFAULT] (if one or more is given, they must be given in this order)
2) <meta|CHR>:  Path to metadata file mapping individuals (1st column) to groups (2nd column).
                Header and tab separation expected.
                More individuals in different order than in <file> are ok.

Details

The map file can contain more samples than are present in the contig number file. Additional columns are also accepted.

Value

A PDF file with a box plot, which is color-coded by taxon group if such are provided.

Examples

plot.contig.numbers.R loci_contignumbers.txt samples.mapfile.txt