plot: legend=FALSE gives error

[rdiaz02]

MRE:

library(OncoSimulR)

## From vignette
set.seed(1)
r7b <- rfitness(7, scale = c(1.2, 0, 1))

## Large pop sizes: clonal interference
(sr7b <- oncoSimulIndiv(allFitnessEffects(genotFitness = r7b),
                        model = "McFL",
                        mu = 1e-6,
                        onlyCancer = FALSE,
                        finalTime = 400,
                        initSize = 1e7,
                        keepEvery = 4,
                        detectionSize = 1e10))

plot(sr7b, show = "genotypes")

plot(sr7b, show = "genotypes", legend = FALSE)
## Error in rep(0L, n.legpercol * ncol - n) : invalid 'times' argument

The error occurs in the call to legend. plot.oncosimul does not use legend for anything, but passes it to other functions (via "...").

There are actually two issues:

1. The error
2. That we cannot prevent the legend from being shown. Arguably, this is a feature, not a bug? I mean, what use is the plot if one cannot tell what the things being plotted are?

But then, we should allow users to modify, for example, the font size so as to minimize overlap with plot stuff. The workaround for now is to play with legend.ncols and the y and maybe x axis range (this is also used in the vignette (https://rdiaz02.github.io/OncoSimul/OncoSimulR.html#655_Simulation_with_order_effects_and_McFL_model)

## Workaround
plot(sr7b, show = "genotypes", legend.ncols = 4, ylim = c(0, 2e7))

That workaround really works if we ask for type = "line". Just need to be aware of the scale of the y axis!

plot(sr7b, show = "genotypes",
     legend.ncols = 5, 
     type = "line",
     ylim = c(1, 1e12))

(Issue originally reported by Deyanira Borroto Alburquerque, from PRSTR class 2024-25).