ggseg 2.0.0

This is a major release that simplifies the package architecture by moving atlas data structures and utilities to the ggseg.formats package.

Breaking changes

• ggseg() is now defunct and errors immediately. Use ggplot() + geom_brain() instead.

• Atlas data (dk, aseg) is no longer bundled in ggseg. Atlases are now provided by ggseg.formats and re-exported as functions: dk(), aseg(), tracula(). Code using the bare objects (e.g., atlas = dk) must be updated to atlas = dk().

• The following functions have been removed and are now in ggseg.formats: as_brain_atlas(), is_brain_atlas(), brain_atlas(), brain_regions(), brain_labels(), brain_pal(), brain_pals_info(), ggseg_atlas(), as_ggseg_atlas(), is_ggseg_atlas(), read_freesurfer_stats(), read_freesurfer_table(), read_atlas_files().

• scale_brain2(), scale_fill_brain2(), scale_colour_brain2(), and scale_color_brain2() are deprecated in favour of scale_brain_manual(), scale_fill_brain_manual(), scale_colour_brain_manual(), and scale_color_brain_manual().

• scale_brain(), scale_fill_brain(), scale_colour_brain(), and scale_color_brain() are deprecated. Atlas palettes are now applied automatically by geom_brain().

• The side argument in geom_brain() and position_brain() has been renamed to view.

New features

• New annotate_brain() function adds view labels (e.g., “left lateral”) to brain plots, respecting the layout from position_brain().

• New scale_brain_manual() family for applying custom named colour palettes to brain plots.

• position_brain() gains nrow, ncol, and views arguments for grid-based layout control of subcortical and tract atlases.

• adapt_scales() now accepts atlas objects directly (not just pre-converted coordinate data frames), and handles "tract" atlas types alongside subcortical.

• geom_brain() now automatically applies the atlas colour palette when no fill aesthetic is mapped.

Improvements

• Messaging uses cli for all user-facing output (brain_join() warnings and info messages).

• Rewrote and reorganised all vignettes with updated examples and renamed files for cleaner URLs.

• Added tracula (white matter tract) atlas as a re-export from ggseg.formats.

ggseg 1.6

ggseg 1.6.8

• Increased C++ standard to C++17 to comply with CRAN policies

ggseg 1.6.7

• Fixed testthat issues with latest version of testthat
• Fixed vignette build issues on CRAN
• removed sf minimum version requirement

ggseg 1.6.5

• Bump version to 1.6.5
• rm freesurfer dep
• rm old remnants
• update readme img
• switch cerebellum labels for wm, gm, fix #80
• fix aseg labels to original, fix #78
• add vis as categorical. fix #76
• change aseg data class , fix #56
• bump version, small CRAN fixes
• add sysreq
• fix axial to coronal in vignette
• change axial to coronal in aseg data
• re-add ggplot2 depends

1.6.4

• Added options hemi and side to geom
• improved position_brain() to accept character vector, and also support subcortical atlases
• Altered axial to coronal in aseg atlas

1.6.3.01

• fixed broken geom after changes to ggplot2 internals
  
• fixed spelling mistakes in docs

ggseg 1.6.3

• removed function to display ggseg palettes
• preparations for CRAN submission
  • added examples to more functions
  • updated links

ggseg 1.6.02

• bug fixes in atlas objects and method internals
• tests in vdiffr
• vctrs class for polygon ggseg data

ggseg 1.6.02

• No longer depends on ggplot2, but imports it.
  • as is advised practice
  • users must explicitly load ggplot2 to access further ggplot2 functions

ggseg 1.6.01

• fixed installation issues by making sure package depends on R>3.3 for polygon holes.

ggseg 1.6.00

New large update, many new features. Of particular note is the introduction of the brain sf geom, which improved speed, and adaptability of the plots.

• ggseg() will stay for a while, but is superseded by a simple features geom
  
• geom_brain introduced as a new function to plot the atlas data
  • an sf geom provides a lot of new features to the package
    
  • more control over display of the slices through position_brain()
    
  • improved capabilities for atlases with regions that have holes
    
• new atlas class brain_atlas which contains simple features data
  
• new functions to allow compatibility between sf and polygon data
  
• utility functions to use on the atlas data for easy access to information
  • plot() functions for ggseg_atlas and brain_atlas classes for a quick look at atlases
    
  • brain_regions functions to easily extract the unique names of regions for an atlas
    
  • improved print method for atlases classes ggseg_atlas and brain_atlas

ggseg 1.5

ggseg 1.5.5

• dk atlas regions renamed to better reflect correct naming
  • pre central and post central are precentral and postcentral
    
• dk atlas now also includes the corpus callosum, as the original atlas contains

ggseg 1.5

ggseg 1.5.4

• dkt renamed to dk
  • the dkt (Desikan-Killiany-Tourville) atlas is not yet available
    
• atlas columns area renamed to region
  • to avoid confusion with the calculation of cortical/surface area
    
• dk atlas region name “medial orbito frontal” changed to “medial orbitofrontal”

ggseg 1.5.3

• Split ggseg, and ggseg3d into two different packages

ggseg 1.5.2

• Adapted to work with dplyr 0.8.1

ggseg 1.5.1

• Changed ggseg_atlas-class to have nested columns for easier viewing and wrangling

ggseg 1.5

• Changed atlas.info to function atlas_info()

• Changed brain.pal to function brain_pal()

• Changed atlas.info to function atlas_info()

• Reduced code necessary for brain_pals_info

• Simplified display_brain_pal()

• Moved palettes of ggsegExtra atlases to ggsegExtra package

• Added a NEWS.md file to track changes to the package.

• Added compatibility with grouped data.frames

• Reduced internal atlases, to improve CRAN compatibility

• Added function to install extra atlases from github easily

• Changes vignettes to comply with new functionality