Pyramid annotations

[teunbrand]

Pyramid plots now have an edge by default:

pyramid(exp, "chr1", 30e6, 40e6)

The edge follows cropping and is customisable:

pyramid(exp, "chr1", 30e6, 40e6, 
        crop_x = c(315e5, 385e5), crop_y = c(0, 5e6),
        edge = grid::gpar(col = "blue", lty = 2))

There are also classic CTCF site annotations:

p <- pyramid(exp, "chr1", 30e6, 40e6)
p + add_ctcf_sites(ctcf_bed, strand = ctcf_bed[, 4], size = 1)

Compartment scores, insulation scores and directionality indices can be displayed as tracks by adding them to the plot.

cs <- compartment_score(explist, bed = H3K4me1)
p + cs

You can exercise more precise control over them if you use as_track() on them:

p + as_track(cs, height = 0.2, geom = "line", linetype = 2)

Domainograms and virtual 4Cs are added as seperate tracks:

domain <- insulation_domainogram(explist, "chr1", 30e6, 40e6)
p + domain

You can add regular ggplot2 layers as long as some data value falls between the start and end of the pyramid plot:

x <- seq(20, 50, by = 0.1) * 1e6
df <- data.frame(
  x = x,
  ymin = cumsum(rnorm(length(x))),
  ymax = cumsum(rnorm(length(x)))
)
lay <- ggplot2::geom_ribbon(aes(x, ymin = ymin, ymax = ymax),
                            data = df)
p + as_track(lay, name = "ribbon")

Also, you can stack whatever annotations you want:

p + as_track(lay, name = "ribbon") + 
  domain + 
  add_ctcf_sites(ctcf_bed, strand = ctcf_bed[, 4], size = 1) +
  cs

The disappearing y-axis on the compartment score is currently a bug.

[teunbrand]

I think the check failed because of some pdf/latex/vignette stuff. @robinweide are you ok with merging this anyway?

[robinweide]

First of all, really nice work. It looks very tidy and I like the annotations. Seems like we now have two matrixplotters, which is not bad per se.

I think the check failed because of some pdf/latex/vignette stuff. @robinweide are you ok with merging this anyway?

No, we should fix it. The errors are all about this:

! Package pdftex.def Error: File `colour\T1\textunderscorehot.png' not found.

Let's try to find were you put underscores (or the colour "hot"). It would be ashame to have to ditch the travis-badge.

[teunbrand]

They are in man/figures/colour_hot.png, which I used in ?GENOVA_colours in colours.R. I made these so that the manual displays the colours, but I had to use markdown formatting for that doc to get these to work (which looks fine in the html docs). Perhaps we should revert to less fancy formatting and use branching logic instead, for example the one we use for the subscript '2' in log2: \ifelse{html}{\out{log<sub>2</sub>}}{\eqn{log_2}}