8000 geom_brain() plots dorsal/ventral sides when present in an atlas by monicathieu · Pull Request #108 · ggseg/ggseg · GitHub
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geom_brain() plots dorsal/ventral sides when present in an atlas #108

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geom_brain() plots dorsal/ventral sides when present in an atlas #108

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This is almost the final PR for dorsal/ventral ggseg atlas support! This, along with using updated atlases generated with the associated update of ggsegExtra, would close #74 . I have tested it locally on a tentative update of the ggsegGlasser atlas (because I needed that atlas specifically for my current study).

Major changes:

  • geom_brain() works as expected (ish, see below) when an atlas including dorsal and ventral sides is used!!!
    • Shows dorsal and ventral views with frontal pole on top, at 12 o'clock (see upstream functionality)
    • position_brain() should behave the same on existing atlases with only lat/med views (and subcort atlases).
    • For atlases with lat/med/dors/vent views, position_brain() handles them in the following ways:
      • when position is a grid formula,stack_grid() now stacks either 2x4 or 4x2
      • when position is horizontal or vertical, default_order() now expects dorsal/ventral views and spaces them properly, putting dorsal and ventral as the 3rd and 4th sides in the order

Minor changes:

  • side argument of geom_brain() can now take a vector of sides by way of calling match.arg(several.ok = TRUE). I imagine this functionality didn't make sense before with only 2 sides in cortical atlases, but with 4 possible sides now it makes sense to pick 2.

Remaining bugs/weirdness:

  • The biggest thing is that plots mixing lat/med and dors/vent views look funky, with the dors/vent hemispheres being weirdly far from one another. The reason is that the internal function get_sep() uses the max bounding box across hemispheres, and since the dors/vent hemispheres are narrow in the x direction, they look very far from one another when placed using the bounding box for the lat/med hemispheres. I didn't want to change the functionality of get_sep(), so I'm leaving this weirdness in to see if you or a 8000 nyone else have a better idea of how to deal with it.
    • The weirdness can be temporarily worked around by calling geom_brain(side = c('dorsal', 'ventral')) (or with either dorsal or ventral alone). When only "narrow" hemispheres are included, they get spaced appropriately closer together.
  • testthat tests for scale-brain are failing because the old plot snapshots don't have any NA scale_fill/colour_brain values, but when I R CMD check on my local machine, the atlases being called do have parcels that aren't being mapped to a scale value. I haven't chased this down that closely (I didn't modify any of the atlases called in the test??) but I can if it's important that that test pass as it was. Local R CMD check throws no other errors.

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Superior and inferior views of the dk brain
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