Graphics

Momocs2 as a shape manipulation and morphometrics package is chiefly (and pretty much only) concerned with plotting shape(s).

Momocs2 graphics all use ggplot2 graphics (todo link Mombook) and, where that makes sense, use tidyevaluation (todo link Mombook).

Momocs2 graphical methods try hard to use minimal but sensible default. I do not want to have functions with 50 arguments, that would anyway be redundant due to their ggplot2 nature. If you want to change something, just start from a recipe here, or do it yourself using ggplot2 methods.

Each object have a default method, that can be obtained with the good old plot. I realize that is really heretic to use plot() to obtain ggplot2, but I think it’s simple and useful.

Plotting shapes

pile

pile is the default method for shape(s):

bot %>% pick(1) %>% pile()

bot$coo %>% pile()

bot %>% pile()

mosaic

inspect

Plotting coefficients

Other graphics

Technical aspects

All graphics are ggplot2 graphics

All MomX, and thus Momocs2, graphics rely on ggplot2. If you do not know it at all, or do not master it yet, there is nothing to be afraid of, really. An by the way, you do not need extensive ggplot2, recipes below are likely to cover your needs.

I do not want to enter the infinite and slippery discussion of “why ggplot2”: just like anything else, ggplot2 has its detractors and evagelists. I obviously fall more in the second category for several reasons:

  • Its graphics are beautiful and if yours suck, it is likely not ggplot2 fault.
  • It is “smart” because of the grammar it relies on. If there is somewhere I really want a grammar it is graphics. Did you really like legend()?
  • Its learning curve is steep, mostly the, say, first 20 hours. But these first moments will be fulled of “wow” moments.
  • Time invested will be funded back quickly and forever.
  • Do not think there are things you cannot do with ggplot2 just because it want a tibble to start with.
  • There are many extensions
  • The user community is huge, so it is very likely that your problem has already been adressed, eg on StackOverflow

Overall, I think using ggplot2 as the main graphics engine in MomX is a good choice and if you do not agree, it is likely because you think you can do better from scratch, so do not chew the cud and go ahead ;-)