Invert the Density Map

[IdoBar]

Hi,

Thank you for the great package, I have a couple of requests:

1. Can the density map be inverted, i.e. show the Loci/cM, it makes more sense to me and the higher density will be reflected by "hotter" colours, I'll put a PR for that one.
2. When trying to create a larger density map by expanding the PDF canvas (to show the linkage groups with higher resolution), the density bar plot gets extended (see image), is it possible to "lock" its height?

Thanks, Ido

[sgblanch]

Ido,

I agree. Reporting density as cM/Locus is a bit confusing. That was the way we'd seen 'density' reported on the linkage maps that identified the need for LinkageMapView. We've also seen cM/Locus reported in literature. The current 'density' is probably better termed 'distance between loci' or even 'map resolution'. (Both terms also show up in literature).

It should be relatively easy to add an inverted density (i.e. true density) to LinkageMapView. Since the current density map is provided by a user-called function it will be trivial to provide a second function that generates the density map in loci/units.

For (2), your best bet right now is to let LinkageMapView decide the canvas size and then scale the output PDF to the size you need. As long as the largest linkage group is under 1000 units, LinkageMapView uses a step size of one unit to compute density so the density in the PDF should scale well. Depending on how much you need to scale the PDF, you might need to adjust font sizes (*cex*, pdf.pointsize), line widths (*lwd*), chromosome width (lgw), etc.

Thanks,
~Steven