gl.report.pa map info?

[Mike Patrick]

Is there any info on how the interactive map generated by gl.report.pa() is generated/how to interpret/etc? I've checked the documentation, but it's kind of sparse and there's no legend so I just want to be sure I'm not making too many assumptions.

MP

[Jose Luis Mijangos]

Hi MP,

When map.interactive = TRUE and method = "pairwise", gl.report.pa() calls gl.map.interactive() to draw the map. It does this:

- Plots each population at the mean of its gl@other$latlon coordinates, labelled by population name. Populations without coordinates are skipped.

- Joins pairs with asymmetric arrows. The arrow value is the count of alleles private to the population at the tip relative to the one at the base (the priv1 and priv2 columns in the returned table).

- Draws only the larger of the two reciprocal counts per pair, so an arrow A -> B means B has more private alleles relative to A than A has relative to B.

- Rescales arrow widths to 1-10 from the min and max of the full pairwise matrix, so they are relative, not absolute.

No legend is shown because the widths are standardised. For the raw counts, use priv1 and priv2 in the returned data frame.

Cheers,

Luis

[Mike Patrick]

Perfect, thanks for the info.