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ggbrain

R package for creating plots of brains using ggplot.

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Version

Install

install.packages('ggbrain')

Monthly Downloads

438

Version

0.9.0

License

GPL (>= 3)

Maintainer

Michael Hallquist

Last Published

March 20th, 2025

Functions in ggbrain (0.9.0)

geom_region_label

Variant of geom_label used for plotting region labels on slices

Generic R6 base class that is used to support + semantics

geom_region_text

Variant of geom_text used for plotting region labels on slices

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

create ggb container object for a given plot

Adds a raster layer to the ggbrain plot, displaying pixels from the specified layer definition

R6 class for adding labels to a ggbrain_panel

geom_region_text_repel

Variant of geom_text_repel used for plotting region labels on slices with separation from other labels

R6 class for compiling images to render in ggplot

geom_region_label_repel

Variant of geom_label_repel used for plotting region labels on slices with separation from other labels

Add images to a ggbrain object

ggplot_add.ggbrain_panel

S3 method to support adding ggbrain_layer objects to an existing ggplot object

ggbrain_layer_brain

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

ggplot_add.ggbrain_layer

S3 method to support adding ggbrain_layer objects to an existing ggplot object

R6 class for a single panel of a ggbrain image

ggbrain_layer_outline

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

R6 class for managing slice data for ggbrain plots

ggplot_add.ggbrain_label

S3 method to support adding ggbrain_label objects to an existing ggplot object

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

R6 class for a single layer of a ggbrain panel

breaks function to encourage integer-valued breaks, based on input from pretty

S3 method to allow for plot(x) syntax with ggbrain (ggb) objects

Finds the nearest non-missing neighbors of a target point in a 2D matrix

plot.ggbrain_panel

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

Finds the mode of an integer vector

little helper function to create named list from objects

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

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

plot.ggbrain_patchwork

S3 method to allow for plot() syntax with rendered ggbrain patchwork objects

scale_fill_bisided

scale for plotting separate color gradients for positive and negative values

Adds slices to the ggbrain plot, including additional panel aesthetics

Fast conversion of 2D mat to 3-column data.frame with dim1, dim2, value

Function to convert ggb object to ggplot/patchwork object

S3 method to allow for render(x) syntax with ggbrain (ggb) objects

+.ggbrain_images

summary S3 method for ggbrain_images objects addition operator for combining ggbrain_images objects

Sort Matrix by Column

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

addition operator for ggb object to support ggplot-like syntax

plot.ggbrain_plot

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

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

Adds contrast definitions to the ggbrain plot

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

count_neighbors

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

annotate_coordinates

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

Convert a 3-column data.frame (dim1, dim2, value) to a 2-D matrix

contrast_parser

helper function to calculate contrasts of one or more images using a combination of image arithmetic and logical subsetting

helper function to center a numeric matrix within a (larger) target matrix size

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

Adds custom annotations to a single panel on the ggbrain plot