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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

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.