I managed to figure it out myself. I guess apply does not work for genotype objects, so I used lapply followed by do.call instead. Not sure if this was due to my lack of R skills or if there is actually an error in the 'genetics' package. Hope this helps somebody...

If you're working with a matrix you can implement heatmap() or heatmap2()

 library(gplots)
 heatmap2(matrix)

That's pretty much it. ggplots2 also has a correlation matrix function

library(ggplot2)
library(corrplot)
corrplot(matrix)

There's lots of options in R for heatmaps/correlation matrices. The documentation is very useful too.