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Changelog

Source: NEWS.md

ggbrain 0.8.2 (DEVELOPMENT)

  • 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

ggbrain 0.8.1 (21Mar2023)

CRAN release: 2023-03-21

  • 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