# Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax

## Documentation for package ‘ggbrain’ version 0.9.1

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

+.ggb | addition operator for ggb object to support ggplot-like syntax
+.ggbrain_images | summary S3 method for ggbrain_images objects addition operator for combining ggbrain_images objects
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_slice | 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(x) syntax with ggbrain (ggb) objects
plot.ggbrain_panel | S3 method to allow for plot() syntax with ggbrain_panel objects
plot.ggbrain_patchwork | S3 method to allow for plot() syntax with rendered ggbrain patchwork objects
plot.ggbrain_plot | S3 method to allow for plot() syntax with ggbrain_panel objects
print.ggbrain_patchwork | S3 method to allow for plot() syntax with rendered ggbrain patchwork 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
render.ggb | S3 method to allow for render(x) syntax with ggbrain (ggb) objects
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