Modification of plot2D to allow filled characters

[lmsimp]

I would like to add functionality to plot2D to allow the use of filled point characters. Currently, it is not easy to straightforward to implement with ... which is passed to points in the plot2D code.

I would explicitly like to add an argument bg to plot2D (as it is used in points) and add functions getStockbg, setStockbg to work in the same way we currently have for col and setting marker colours.

I have already an amended version of plot2D I use that allows this and would like to submit a PR to update the version we have in pRoloc.

As discussed with you at Bioc eventually we may default to using ggplot for generating maps but plot2D is still very much used day-to-day in the lab and I think it is a great function that works out of the box within the pRoloc workflow.

Are you happy for me to add this and submit a PR? I will also add appropriate unit tests.

CC @Charl-Hutchings

[lgatto]

Does your update break any existing code? If not, then, I think it could be added. If there more risky changes, unit tests that tests the previous and new behaviour would be good.

[lmsimp]

No existing code is broken. I think all is okay. I will check the vignettes.

I want to also change some of the default behaviour such as the call to grid and change it from grid = TRUE to grid = FALSE. Can I just change this or do I need some interim step to warn users the default behaviour has changed?

In any case, I will wait for @Charl-Hutchings to submit her PR for markers next week before adding this to a branch and submitting a PR.

[lgatto]

Not that (some of) the plot2D will hopefully become obsolete after the refactoring to SE, as it'll be possible to easily get a long table to use ggplot() on the fly.

[lmsimp]

Yes, it will be really great to be able to pipe output to ggplot on the fly. I have been thinking however it would be nice to keep plot2D alongside using ggplot... but I do realise you are keen to lighten the code load and of avoid redundancy. We will want to at the least keep functionality for computing dimensionality reduction.