A bit of maintenance

[teunbrand]

Should fix #266, allowing the following:

library(GENOVA)

exp <- get_test_data("40k")
ins <- insulation_score(exp, window = 10)
tads <- call_TAD_insulation(ins)[[1]]

feats <- split(tads, sample(1:2, nrow(tads), replace = TRUE))

tornado_insulation(ins, feats)

^{Created on 2021-06-30 by the reprex package (v2.0.0)}

Also fix #268 by allowing the following

# {strand_var} is a character/factor of "+" and "-" of length `nrow(bed)`.
ARA(exp, bed, strand = {strand_var})

Changed cut.off argument in hic_matrixplot() to colour_lim, allow to set both the lower and upper limit (instead of just the upper). The change should be backward compatible, so that cut.off still works. Also added colour_bar = TRUE/FALSE options for the *_matrixplot() family. Together these fix #260.

A proposed modification to the saddle function is implemented, which should fix #263

[teunbrand]

@robinweide I think the build might have failed but I can't see why. Do you have any ideas?

[teunbrand]

I re-checked on my local machine (Windows 10), found a few additional notes that I've resolved. I'm reasonably confident that this should now be OK.