Rescale getBaseTheme for publication sizes

[Jason Vander Heiden]

It should be possible to plot figures from alakazam with font sizes scaled for publication size PDFs (eg 7"x5"). Can pull getBaseTheme() from Salmonella or MG study, perhaps with a plotting option to scale for figure or RStudio window (which needs vastly different sizing). Also, see if the same can be done with line widths and dot sizes.

[Jason Vander Heiden]

Pulled theme from MG figures. Added an option for larger sizing, but without an option to pass it through from plotting functions, as this can be accomplished via the ellipsis arguments. Looks like there is a separate mechanism for aesthetic defaults (update_geom_defaults()).