Function reference • ggbrain

All functions

annotate_coordinates(): Adds the coordinate labels to each panel based on the location of the slice along the slicing axis (e.g., z = 15)

annotate_panel(): Adds custom annotations to a single panel on the ggbrain plot

count_neighbors: This function counts the number of neighboring/touching pixels in a 2D binary image

define(): Adds contrast definitions to the ggbrain plot

fill_from_edge: This function finds holes by flood filling TRUE into a 2D binary image, starting from the edge

find_threads: This function finds 'threads' hanging off of the edges of blobs in an image, allowing the user to trim them

flood_fill: This function flood fills a binary image with TRUE for any value of FALSE

geom_brain(): Adds a raster layer to the ggbrain plot, displaying pixels from the specified layer definition

geom_outline(): Adds an outline layer to the ggbrain plot, displaying outlines from the non-missing pixels in the specified layer definition

geom_region_label(): Variant of geom_label used for plotting region labels on slices

geom_region_label_repel(): Variant of geom_label_repel used for plotting region labels on slices with separation from other labels

geom_region_text(): Variant of geom_text used for plotting region labels on slices

geom_region_text_repel(): Variant of geom_text_repel used for plotting region labels on slices with separation from other labels

ggbrain(): create ggb container object for a given plot

ggbrain_images: R6 class for compiling images to render in ggplot

ggbrain_label: R6 class for adding labels to a ggbrain_panel

ggbrain_layer: R6 class for a single layer of a ggbrain panel

ggbrain_layer_brain: R6 class for a single layer of a ggbrain panel using fill geom

ggbrain_layer_outline: R6 class for a single layer of a ggbrain panel using outline geom

ggbrain_panel: R6 class for a single panel of a ggbrain image

ggbrain_plot: An R6 class for constructing a ggbrain plot from a ggbrain_slices object

ggplot_add(<ggbrain_label>): S3 method to support adding ggbrain_label objects to an existing ggplot object

ggplot_add(<ggbrain_layer>): S3 method to support adding ggbrain_layer objects to an existing ggplot object

ggplot_add(<ggbrain_panel>): S3 method to support adding ggbrain_layer objects to an existing ggplot object

images(): Add images to a ggbrain object

integer_breaks(): breaks function to encourage integer-valued breaks, based on input from pretty

montage(): Convenience function to add many slices in a montage along one of the 3D planes

nn_impute: Imputes missing values in a 2D matrix based on the nearest non-missing neighbors in a given radius

plot(<ggb>): S3 method to allow for plot() syntax with ggbrain (ggb) objects

plot(<ggbrain_panel>): S3 method to allow for plot() syntax with ggbrain_panel objects

plot(<ggbrain_plot>): S3 method to allow for plot() syntax with ggbrain_panel objects

`+`(<ggb>): addition operator for ggb object to support ggplot-like syntax

`+`(<ggbrain_images>): addition operator for combining ggbrain_images objects

range_breaks(): breaks function for including min + max with labels, and a few unlabeled ticks in between

render(): Function to convert ggb object to ggplot/patchwork object

scale_fill_bisided(): scale for plotting separate color gradients for positive and negative values

slices(): Adds slices to the ggbrain plot, including additional panel aesthetics