updated ggplot_add methods to be compatible with ggplot2 4.0
ggbrain 0.9.0 (18Mar2025)
notice: annotate_panel is now called annotate_slice for
consistency
notice: the plot() method now works with rendered and un-rendered
objects, always drawing to the current graphics device
feature: Support use of label columns in contrast specification
feature: Support use of inline factor() specification in aes() for a
geom_outline or geom_brain layer
feature: If layer definition uses := syntax, use the lefthand side
as the layer name when no name is provided
bugfix: Allow for quantile “q” specifications for label position
that can be 1-100 (percentile) or 0-1 (quantile)
bugfix: Do not throw error when contrast specification includes
equals sign (logical tests)
bugfix: Only use := syntax for naming contrasts. For compound
contrast expressions, use = ; =
bugfix: Pass through label_columns as attribute from inline contrast
definitions of the form =
bugfix: Handle fixed fill in ggbrain_layers when alpha < 1
bugfix: retain the order of ordered factors in labels when
unify_scales = TRUE
bugfix: copy through label columns for simple subset contrasts
bugfix: extend background color rectangle to cover entire plot when
legend is large
bugfix: support ggplot2 3.5.0+, working around collision with
ggnewscale for categorical images
ggbrain 0.8.1 (21Mar2023)
feature: ggbrain objects can be added together,
allowing common parts across plots to be reused
feature: geom_outline now supports dilation and erosion
using the dil_ero argument
feature: geom_region_label* and
geom_region_text* now support a min_px
argument that controls the minimum number of pixels on a slice that will
result in a label. Helps reduce labeling of small regions
feature: support aes(outline=, group=) for geom_outline,
allowing for subdivision of outlines
bugfix: add workaround for show.legend bug when there are multiple
fill layers: https://github.com/eliocamp/ggnewscale/issues/32
bugfix: switch to linewidth instead of size for borders in
ggbrain_panel object
bugfix: default to cyan color (with message) if geom_outline is
added without any color information
bugfix: correction to pass forward data.frame after
fill_holes algorithm is applied
bugfix: nn interpolation for fill_holes now takes the
mean of neighbors for continuous-valued data
bugfix: use the correct fill column when using
remove_specks for a categorical image
ggbrain 0.8 (21Oct2022)
first public release of the package to CRAN (hooray!)
feature: add define() function to support contrast
definition in ggbrain pipeline outside of a given layer
feature: fixed fill colors are now supported in
geom_brain using
geom_brain(fill='color_here')
feature: images() supports a volumes
argument so that volumes from 4-D images can be visualized
feature: plot() on a ggbrain object supports
guides argument that passes to plot_layout()
in patchwork. Also, the default is now
guides="collect", which combines shared legends.
feature: support min_coord and max_coord
in montage function for coordinate-based ranges
update: archive ggbrain_legacy and remove cowplot dependency
update: add_images() is now images() for
nonredundancy
update: add_slices() is now slices() for
nonredundancy
update: renamed outline_size to just size
in geom_outline for consistency with ggplot2 logic (e.g.,
geom_contour).
update: removed add_slice() in favor of
slices(). If attributes such as bg_color are
set by slices(), these will be the same for each slice in
the operation.
bugfix: properly display geom_outline for continuous
images
ggbrain 0.7 (23Sep2022)
feature: abstract fill_holes,
trim_threads, and remove_specks to
ggbrain_layer – exposed in geom_brain and
geom_outline. This allows these modifications to be made
for contrast layers.
feature: fill_holes now supported in geom_brain and
geom_outline objects. Uses flood fill algorithm to find
interior holes, then uses nearest neighbor imputation, taking the mode
for categorical images and mean for continuous images.
feature: for annotations, q syntax now allows for quantiles
above 1 or below 0, where 2 = 200% of max and -1 is -100% of min. This
allows for annotations to be placed outside of image boundaries.
feature: implement Rcpp-based flood fill algorithm for finding
interior holes on slices. Used for fill_holes.
feature: implement Rcpp-based pixel neighbor counting algorithm to
clean up frayed edges of outlines and fills.
feature: switch to Rcpp mat2df function instead of reshape2::melt
for speed. Remove reshape2 dependency
bugfix: when geom_raster is provided with alpha and
na.value=‘transparent’, it draws semi-transparent squares. Switched to
na.omit() when alpha < 1.
bugfix: ggbrain_slices still returns data for layers that are all NA
so that layers are not dropped from range calculations.
bugfix: do not add a ggbrain_layer to a plot if all of its values
are NA. Adds all_na field.
bugfix: properly handle ggbrain_images filter when an integer vector
is provided
bugfix: fix simple_subset for contrast_parser when there are no
brackets in the expression
bugfix: correct contrast_parser for conjunctions so that both
numeric value and label are returned. Also now use := syntax for
values.
bugfix: fully remove assumption of “label” column in categorical
layers, fixing calculation of unique values in each categorical
layer
bugfix: convert NAs to 0s within contrast parsing so that numeric
logical comparisons always yield TRUE/FALSE and not NA.
ggbrain 0.6 (9Aug2022)
feature: for labeled images, clean_specks now counts specks by
ROI/mask value
feature: support filter expression in add_image() to filter (subset)
the data for a given image. Useful for thresholding or for subsetting an
atlas to retain only certain values.
feature: montage() function to make adding many slices in a plane
easy
feature: support plot() on ggbrain() objects so that the ggbrain
settings can be amended prior to the render and plot steps
feature: support overall plot aesthetics including title, base_size,
bg_color, and text_color. These are arguments to ggbrain()
feature: set tiny values on each slice to NA to support transparency
at image boundaries (e.g., in ‘dead space’ on a structural)
feature: add_slice() function adds single slice and supports
panel-specific aesthetics such as title and text_color
feature: contrasts that are simple subsetting operation on a labeled
image retain labels in the contrast data
bugfix: correct accidental resetting of unified scale limits when a
bisided scale was empty on one side
bugfix: correct range_breaks() for empty data
bugfix: pass through breaks to layers regardless of whether scale or
breaks are set first
bugfix: cleaning specks no longer fails when a slice is empty
bugfix: refactor outlines so that empty slices do not generate
completely filled layer
ggbrain 0.5.1 (2Aug2022)
abstract geom_brain and geom_outline to different R6 classes that
inherit from ggbrain_layer
support blur_edge to allow for blurred outlines that are less
jagged
support clean_specks = to remove regions of this size or
smaller from slices
support alpha transparency in geom_brain and geom_outline layers
with alpha=<number> syntax
support control of how outlines are grouped/calculated in labeled
images using
geom_outline(mapping=aes(group=<label_col>))
bugfix: allow for empty annotations in overall plot