Improve documentation for visualization

[cvanderaa]

We should explicitly document in the vignette how to make additional useful visualisation. Current ideas:

Intensity plot

Show peptide/protein intensities vs other covariates. Eg (from scplainer article):

Code to make this plot:

i <- "APNVVVTR"
df <- data.frame(logIntensity = scpModelInput(sce)[i, ], colData(sce))
ggplot(df) +
        aes(x = Set, y = logIntensity, colour = SampleType) +
        ...ggplot beauty...

Dynamic range plot

Show the distribution of peptide/protein baseline. Eg (from Guise et al. 2024, Cell Rep.):

Code to make this plot (without cell type colouring):

x <- scpModelIntercept(sce)
df <- data.frame(baseline = x, rank = order(x))
ggplot(df) +
        aes(x = rank, y = baseline) +
        ...ggplot beauty...

If we want to include cell types colouring (or another variable), this will become a little more intricate as we need to extract the population effects form the effect matrix of interest.