NEWS.md

In michaelhallquist/ggbrain: Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax

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

ggbrain 0.5 (29Jul2022)

• Initial internal release of ggbrain package

michaelhallquist/ggbrain documentation built on June 11, 2025, 12:47 a.m.