Type: Package
Title: Create Images of Volumetric Brain Data in NIfTI Format Using 'ggplot2' Syntax
Version: 0.9.0
Date: 2025-03-18
Maintainer: Michael Hallquist <michael.hallquist@gmail.com>
Description: A 'ggplot2'-consistent approach to generating 2D displays of volumetric brain imaging data. Display data from multiple NIfTI images using standard 'ggplot2' conventions such scales, limits, and themes to control the appearance of displays. The resulting plots are returned as 'patchwork' objects, inheriting from 'ggplot', allowing for any standard modifications of display aesthetics supported by 'ggplot2'.
URL: https://michaelhallquist.github.io/ggbrain/
BugReports: https://github.com/michaelhallquist/ggbrain/issues
Depends: R (≥ 3.5.0)
Imports: Matrix, RNifti, checkmate, data.table, dplyr, ggplot2, ggnewscale, ggrepel, glue, imager, patchwork, rlang, tibble, tidyr, tidyselect, Rcpp
Suggests: knitr, rmarkdown
License: GPL (≥ 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2025-03-19 02:05:10 UTC; hallquist
Author: Michael Hallquist ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2025-03-20 01:30:02 UTC

addition operator for ggb object to support ggplot-like syntax

Description

addition operator for ggb object to support ggplot-like syntax

Usage

## S3 method for class 'ggb'
o1 + o2

Arguments

o1

the first object inheriting the ggb class

o2

the second object inheriting the ggb class

Details

Note that the addition operator always clones the underlying o1 object rather than modifying it in place

Value

a modified version of the o1 object with o2 added to it

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

Description

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

Usage

## S3 method for class 'ggbrain_images'
o1 + o2

Arguments

o1

first ggbrain_images object

o2

second ggbrain_images object

Details

note that the addition does not modify either existing object. Rather, the first object is cloned and the second is added to it. If you want to add one ggbrain_images object to another in place (i.e., modifying the extant object), use the $add() method.

Value

combined ggbrain_images object

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

Description

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

Usage

annotate_coordinates(x = "right", y = "bottom", ...)

Arguments

x

the x position of the coordinate label. If numeric, it is assumed to be the pixel position along the x axis (e.g., 26). In addition, convenience values of "left", "right", or "q[1-100]" can be used to look up the left-most, right-most, or quantile-based positions along the x axis.

y

the y position of the coordinate label. If numeric, it is assumed to be the pixel position along the y axis (e.g., 26). In addition, convenience values of 'top', "bottom", or "q[1-100]" can be used to look up the top-most, bottom-most, or quantile-based positions along the y axis.

...

any other arguments to ggplot2::annotate, which will be passed through to each panel

Value

a ggb object with the action 'add_annotations', used in a ggbrain addition chain

Adds custom annotations to a single panel on the ggbrain plot

Description

Adds custom annotations to a single panel on the ggbrain plot

Usage

annotate_slice(slice_index = NULL, ...)

Arguments

slice_index

the slice number to which this annotation is added. These are numbered in the wrapping order from patchwork::wrap_plots, which will normally go from top-left to bottom-right.

...

Additional parameters passed to ggplot2::annotate such as label or geom

Details

For annotation coordinates such as x, y, or xmin, you may pass in a number. In this case, the value specifies the pixel position along the relevant axis (e.g., x=26). In addition, convenience values of 'left', 'right', and 'middle' can be used for the x axis, and 'top', 'bottom', and 'middle' for the y axis.

Finally, or 'q[1-100]' can be used to look up the quantile-based positions along the relevant axis. For example, x="q25" would position the annotation at the 25% mark along the x axis.

N.B. This function only adds a single annotation on a single panel!

Value

a ggb object with the relevant annotations field and an action of "add_annotations"

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

Description

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

Usage

center_matrix(output_dim, mat, default_value = NA_real_, drop_zeros = TRUE)

Arguments

output_dim

the desired dimensions of the output matrix

mat

the 2D numeric matrix containing values to be centered in the output matrix

default_value

the value that should fill padded rows and columns of the output matrix

drop_zeros

if TRUE, all zero-valued rows and columns of mat will be dropped before the data are centered within the output matrix. This is useful if the matrix is asymmetric, but you still want to have it be dead-center in the output.

Value

an expanded matrix of size output_dim with the input matrix mat centered within it.

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

Description

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

Usage

contrast_parser(expr, data = NULL, default_val = NA_real_)

Arguments

expr

a string or expression containing the image calculation to be performed

data

a data.frame containing all variables used in expr. This will be used to perform contrast calculations

default_val

the value to be returned for any element of the contrast calculation that does not pass through the arithmetic, either because of logical subsetting or because it is exactly zero. In general, leave this as NA_real_ unless you know what you're doing.

Author(s)

Michael Hallquist

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

Description

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

Arguments

im

A boolean matrix representing a binary image

diagonal

Whether to count diagonal elements as valid neighbors

Details

This is an internal function used by geom_outline to clean up outlines

Value

A matrix of the same size as im containing the number of neighboring pixels

Author(s)

Michael Hallquist

Adds contrast definitions to the ggbrain plot

Description

Adds contrast definitions to the ggbrain plot

Usage

define(contrasts = NULL)

Arguments

contrasts

a character vector or list containing contrasts to be computed as part of the ggbrain object definition.

Details

contrasts must take the form of ⁠<name> := <value expression>⁠ or must use a named vector. Note that defining a contrast does not directly impact the appearance of the plot unless the contrast is named in a geom_* layer.

Also note that contrasts can be specified in the definition of a layer. Thus, the define function has two primary virtues. First, it allows for the conceptual separation of contrast definition versus usage inside a geom_* layer, which is particularly useful if a contrast is used across several layers. Second, it allows downstream layers to further modify the contrast, such as when we compute a

Value

a ggb object with the relevant contrasts and an action of 'add_contrasts'

Examples

  # T1-weighted template
  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")

  # signed reward prediction error map
  signed_pe <- system.file("extdata", "pe_ptfce_fwep_0.05_2mm.nii.gz", package = "ggbrain")

  # unsigned (absolute value) prediction error map
  abspe <- system.file("extdata", "abspe_ptfce_fwep_0.05_2mm.nii.gz", package = "ggbrain")

  # simple example of a difference contrast, separating definition from usage in geom_brain
  gg_obj <- ggbrain() +
    images(c(underlay = t1, signed_pe = signed_pe, abspe = abspe)) +
    slices(c("x = 25%", "x = 75%")) +
    define("signed_gt_abs := signed_pe - abspe") +
    geom_brain("signed_gt_abs")

  # you can also use a named vector in define(), which is equivalent
  gg_obj <- ggbrain() +
    images(c(underlay = t1, signed_pe = signed_pe, abspe = abspe)) +
    slices(c("x = 25%", "x = 75%")) +
    define(c(signed_gt_abs = "signed_pe - abspe")) +
    geom_brain("signed_gt_abs")

  # contrast definitions can also occur inline, yielding equivalent plots
  gg_obj <- ggbrain() +
    images(c(underlay = t1, signed_pe = signed_pe, abspe = abspe)) +
    slices(c("x = 25%", "x = 75%")) +
    geom_brain("signed_pe - abspe")

  # The use of contrasts() is helpful when layers modify the contrast (e.g., subsetting)
  gg_obj <- ggbrain() +
    images(c(underlay = t1, signed_pe = signed_pe, abspe = abspe)) +
    slices(c("x = 25%", "x = 75%")) +
    define(c(signed_gt_abs = "signed_pe - abspe")) +
    geom_brain(
      "signed_gt_abs[signed_gt_abs > 0]",
      fill_scale=ggplot2::scale_fill_distiller("Pos diff", palette = "Reds")
    )

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

Description

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

Arguments

df

A data.frame representing a melted 2-D matrix, having columns dim1, dim2, and value

replace_na

if not NULL, this numeric value will be used to replace any NAs in df in the resulting matrix. This is useful if downstream code is not built to handle missing values.

Details

There is virtually no input validation of df. You must pass a data.frame that has dim1, dim2, and value as columns. Otherwise, it will not work as expected.

This is a much faster version of the acast function from reshape2 that works only on 2-D matrix conversions.

Value

The matrix form of the keyed data.frame object

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

Description

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

Arguments

im

A boolean matrix representing a binary image

nedges

An integer specifying how many starting points along the edge to use for filling TRUE. The starts are northwest (1), southwest (2), southeast (3), and northeast (4). The compute time increases with the number of starts.

Details

This is an internal function used by geom_outline to clean up outlines

Value

A matrix of the same size as im containing the number of neighboring pixels

Author(s)

Michael Hallquist

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

Description

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

Arguments

im

A numeric matrix representing an image, with non-zero values representing pixels to display

min_neighbors

the minimum number of neighbors a pixel must have to be retained

maxit

the maximum number of iterations to run the thread trimming algorithm. Default: 15.

diagonal

Whether to count diagonal elements as valid neighbors

Details

This algorithm runs count_neighbors iteratively until no pixel exceeds the trimming threshold min_neighbors or the maximum number of iterations, maxit, is reached.

By running iteratively, long tails are trimmed sequentially by pruning the most disconnected voxels.

Value

A logical matrix matrix of the same size as im containing the number of neighboring pixels

Author(s)

Michael Hallquist

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

Description

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

Arguments

im

A boolean matrix reference representing a binary image

x

the starting x position for fill

y

the starting y position for fill

r

the number of rows in im

c

the number of columns in im

Details

This is an internal function used by geom_outline to clean up outlines

Value

Nothing. The matrix im is modified in place (by reference)

Author(s)

Michael Hallquist

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

Description

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

Usage

geom_brain(
  definition = NULL,
  name = NULL,
  fill = NULL,
  fill_scale = NULL,
  mapping = NULL,
  limits = NULL,
  breaks = NULL,
  show_legend = TRUE,
  interpolate = FALSE,
  unify_scales = TRUE,
  alpha = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL
)

Arguments

definition

a character string of the contrast or image definition used to define this layer. Can be a simple image name (e.g., 'underlay') or a contrast string (e.g., 'overlay[overlay > 5]')

name

the name of this layer, used for referencing in layer and panel modifications

fill

A character string indicating the color used to fill all non-NA pixels in this layer. This is used to set the fill color, in distinction to color mapping: mapping=aes(fill=<variable>).

fill_scale

a ggplot scale_fill_* object used for mapping the fill column to the color of pixels in this layer.

mapping

the aesthetic mapping of the layer data to the display. Should be an aes() object and supports fill (color of filled pixels). Default is aes(fill=value), which maps the numeric value of the layer data to the fill color of the squares at each spatial position. For labeled data, you might use aes(fill=<label_col_name>).

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the fill scale

show_legend

if TRUE, show the fill scale in the plot legend. Default is TRUE, except when 'name="underlay"“

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

a number between 0 and 1 that sets the alpha transparency of this layer. Default: 1

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

An optional positive integer specifying the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation. Default: 0.

remove_specks

An optional positive integer specifying the size of specks (in pixels) to be removed from each slice prior to display. Specks are small clusters that may be distracting and contribute to a 'salt and pepper' appearance.

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel.

Details

Note that the fill_scale and limits must be specified at the time of the geom_brain creation in order for them to be mapped properly within ggplot. Because we overlay many raster layers in a ggplot object that all use the fill aesthetic mapping, it becomes hard to map the color scales after the layer is created using the typical + scale_fill_* syntax, and similarly for scale limits.

Value

a ggb object populated with the relevant geom_brain and the action of 'add_layers'

Examples

  # T1-weighted template
  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")

  # signed reward prediction error map
  signed_pe <- system.file("extdata", "pe_ptfce_fwep_0.05_2mm.nii.gz", package = "ggbrain")

  gg_obj <- ggbrain() +
    images(c(underlay = t1, overlay = signed_pe)) +
    slices(c("x = 25%", "x = 75%")) +
    geom_brain("underlay") +
    geom_brain(definition="overlay[overlay > 1]", fill_scale=ggplot2::scale_fill_viridis_c("pos z"))

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

Description

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

Usage

geom_outline(
  definition = NULL,
  name = NULL,
  outline = NULL,
  outline_scale = NULL,
  mapping = ggplot2::aes(outline = NULL, fill = NULL),
  size = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = FALSE,
  unify_scales = TRUE,
  alpha = 1,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  dil_ero = 0L
)

Arguments

definition

a character string of the contrast or image definition used to define this layer. Can be a simple image name (e.g., 'underlay') or a contrast string (e.g., 'overlay[overlay > 5]')

name

the name of this layer, used for referencing in layer and panel modifications

outline

A character string indicating the color used to draw outlines in this layer. This is used to set the outline color, in distinction to outline color mapping: mapping=aes(outline=<variable>).

outline_scale

a ggplot scale_fill_* object used for mapping the fill column to the color of pixels in this layer.

mapping

the aesthetic mapping of the layer data to the display. Should be an aes() object and supports outline (outline color of pixels). Default is aes(outline=NULL), which uses a set outline color.

size

the size of outlines to be drawn in pixel units. Default: 1

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the fill scale

show_legend

if TRUE, show the fill scale in the plot legend

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

a number between 0 and 1 that sets the alpha transparency of this layer. Default: 1

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

An optional positive integer specifying the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation. Default: 0.

remove_specks

An optional positive integer specifying the size of specks (in pixels) to be removed from each slice prior to display. Specks are small clusters that may be distracting and contribute to a 'salt and pepper' appearance.

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel.

dil_ero

the number of pixels to dilate (> 0) or erode (< 0) the outline for display purposes. Default: 0L

Details

Note that the fill_scale and limits must be specified at the time of the geom_brain creation in order for them to be mapped properly within ggplot. Because we overlay many raster layers in a ggplot object that all use the fill aesthetic mapping, it becomes hard to map the color scales after the layer is created using the typical + scale_fill_* syntax, and similarly for scale limits.

Value

a ggb object populated with the geom_outline layer and the action of 'add_layers'

Examples

  # T1-weighted template
  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")

  # signed reward prediction error map
  signed_pe <- system.file("extdata", "pe_ptfce_fwep_0.05_2mm.nii.gz", package = "ggbrain")

  gg_obj <- ggbrain() +
    images(c(underlay = t1, overlay = signed_pe)) +
    slices(c("x = 25%", "x = 75%")) +
    geom_brain("underlay") +
    geom_outline(definition="overlay[overlay > 2]", outline="cyan")

Variant of geom_label used for plotting region labels on slices

Description

Variant of geom_label used for plotting region labels on slices

Usage

geom_region_label(image, label_column = "label", min_px = 1L, ...)

Arguments

image

The name of the image within the underlying ggbrain_slices object that contains the labeled data positions

label_column

The column name name for the labels to use within the slice data

min_px

The minimum number of pixels present on a slice that will result in a text label. Default: 1

...

All other parameters passed through to geom_label

Value

a ggb object with the relevant ggbrain_label field and an action of "add_region_labels"

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

Description

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

Usage

geom_region_label_repel(image, label_column = "label", min_px = 1L, ...)

Arguments

image

The name of the image within the underlying ggbrain_slices object that contains the labeled data positions

label_column

The column name name for the labels to use within the slice data

min_px

The minimum number of pixels present on a slice that will result in a text label. Default: 1

...

All other parameters passed through to geom_label_repel

Value

a ggb object with the relevant ggbrain_label field and an action of "add_region_labels"

Variant of geom_text used for plotting region labels on slices

Description

Variant of geom_text used for plotting region labels on slices

Usage

geom_region_text(image, label_column = "label", min_px = 1L, ...)

Arguments

image

The name of the image within the underlying ggbrain_slices object that contains the labeled data positions

label_column

The column name name for the labels to use within the slice data

min_px

The minimum number of pixels present on a slice that will result in a text label. Default: 1

...

All other parameters passed through to geom_text

Value

a ggb object with the relevant ggbrain_label field and an action of "add_region_labels"

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

Description

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

Usage

geom_region_text_repel(image, label_column = "label", min_px = 1L, ...)

Arguments

image

The name of the image within the underlying ggbrain_slices object that contains the labeled data positions

label_column

The column name name for the labels to use within the slice data

min_px

The minimum number of pixels present on a slice that will result in a text label. Default: 1

...

All other parameters passed through to geom_text_repel

Value

a ggb object with the relevant ggbrain_label field and an action of "add_region_labels"

Generic R6 base class that is used to support + semantics

Description

Generic R6 base class that is used to support + semantics

Generic R6 base class that is used to support + semantics

Details

this object becomes a simple storage class that contains all relevant objects (e.g., ggbrain_images) required to generate a brain plot

Public fields

ggb_images

ggbrain_images object for this plot

ggb_image_labels

a named list of data.frames that label corresponding images

ggb_slices

list slices to extract for this plot

ggb_contrasts

a character vector of contrasts to be computed as part of this plot

ggb_layers

a list of ggbrain_layer objects containing the bottom-to-top layers to be plotted

ggb_plot

a ggbrain_plot object containing the specification of the plot

ggb_annotations

a list of annotation objects

ggb_region_labels

a list of ggbrain_label objects to be added as text to label regions

action

what should this ggb object contribute to another when added with it?

Methods

Public methods

Method new()

create a new ggb object. Note that inputs are always cloned to avoid unintended modify-in-place behaviors of R6 classes.

Usage
ggb$new(
  images = NULL,
  slices = NULL,
  contrasts = NULL,
  layers = NULL,
  labels = NULL,
  annotations = NULL,
  region_labels = NULL,
  title = NULL,
  bg_color = NULL,
  text_color = NULL,
  base_size = NULL,
  action = NULL
)
Arguments
images

a ggbrain_images object containing relevant images

slices

a character vector of slices to extract

contrasts

a character vector of contrasts to define and compute

layers

a list of ggbrain_layer objects

labels

a list of data.frames with labels that align with one or more images

annotations

a list of data.frames with annotations that will be added to specific slices

region_labels

a list of ggbrain_label objects with text-based labels to be drawn on the plot

title

overall title of the plot

bg_color

the background color of the overall plot

text_color

the text color of the overall plot

base_size

the base size of text on the plot

action

the action to be taken when adding this object to an existing ggb

Method add_layers()

add layers from another ggb object to this one

Usage
ggb$add_layers(ilist)
Arguments
ilist

a list of ggbrain_layer objects. If a ggb object is passed, we will get this list from obj$ggb_layers

Method add_slices()

add slices to the existing vector of slices

Usage
ggb$add_slices(slices = NULL)
Arguments
slices

a character vector of slices to be appended to the existing slices

Method add_contrasts()

add contrast definitions to the plot object

Usage
ggb$add_contrasts(contrasts)
Arguments
contrasts

a character vector of contrasts to compute as part of the plot generation

Method add_annotations()

add annotations to panels

Usage
ggb$add_annotations(annotations = NULL)
Arguments
annotations

a list or data.frame containing the annotations to add to each panel. Minimally, the list or data.frame must contain position and label columns that define the position and text to be added. Other arguments that pass through to ggplot2::annotate() can be provided as columns/elements in annotations and these will be passed through to annotate

Method add_image_labels()

add labels to a given image

Usage
ggb$add_image_labels(...)
Arguments
...

a named list of arguments where each is a data.frame with labels denoting corresponding images

Method add_region_labels()

add a list of ggbrain_label objects to the overall ggb for compiling a plot

Usage
ggb$add_region_labels(labels = NULL)
Arguments
labels

a list of data.frames with region labels that should be plotted on each slice. This is generated internally by ggbrain_images$get_slices() in the $slice_labels field.

Method render()

this method converts the ggb object into a compiled ggplot2 object that can then be passed to other functions from cowplot, ggplot2, and patchwork. Once the object is rendered, it no longer retains the underlying ggb fields that contain the elemental data.

Usage
ggb$render(guides = "collect")
Arguments
guides

Passes through to patchwork::plot_layout to control how legends are combined across plots. The default is "collect", which collects legends within a given nesting level (removes duplicates).

Method plot()

plot this ggb object – just an alias for render

Usage
ggb$plot(guides = "collect")
Arguments
guides

Passes through to patchwork::plot_layout to control how legends are combined across plots. The default is "collect", which collects legends within a given nesting level (removes duplicates).

Details

requires that required elements are in place already.

Method clone()

The objects of this class are cloneable with this method.

Usage
ggb$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

create ggb container object for a given plot

Description

create ggb container object for a given plot

Usage

ggbrain(
  images = NULL,
  slices = NULL,
  title = NULL,
  bg_color = "grey8",
  text_color = "grey92",
  base_size = 14
)

Arguments

images

a character vector or existing ggbrain_images object defining which images should be included in this plot

slices

a set of slices to be added to the plot

title

the overall title to be added to the plot

bg_color

The background color of the overall plot

text_color

The default text color of the overall plot (passes through to panels)

base_size

The base size of fonts used in the plot (cf. theme_minimal)

Value

a ggb object containing basic information for a ggbrain plot such as background color, text color, and font size

R6 class for compiling images to render in ggplot

Description

R6 class for compiling images to render in ggplot

R6 class for compiling images to render in ggplot

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at images().

Value

a ggbrain_images R6 class containing fields related to a set of NIfTI images imported into R

Active bindings

zero_tol

the (positive) numeric value that should be treated as indistinguishable from zero. This value is used to set small values in the images to exactly zero for proper masking. Default 1e-6

slices

a character vector of cached slice specifications to be used in $get_slices()

contrasts

a character vector of cached contrast specifications to be used in $get_slices()

Methods

Public methods

Method new()

create ggbrain_images object consisting of one or more NIfTI images

Usage
ggbrain_images$new(images = NULL, volumes = NULL, labels = NULL, filter = NULL)
Arguments
images

a character vector of file names containing NIfTI images to read

volumes

the volumes to be read from each element of images. By default, this is 1, in which case the first volume is used, which is appropriate for all 3-D images. For 4-D images, volumes gives you more flexibility over the volume to display.

labels

A named list of data.frames with labels that map to values in the integer-valued/atlas elements of images. If a single data.frame is passed, it will be accepted if only a single image is passed, too. These are then assumed to correspond

filter

A named list of filter expressions to be applied to particular images. The names of the list correspond to the names of the images provided. Each element of the list can either be a character vector denoting a filtering expression (e.g., 'value < 100') or a numeric vector denoting values of the image that should be retained (e.g., c(5, 10, 12)).

Method add()

method to add another ggbrain_images object to this one

Usage
ggbrain_images$add(obj)
Arguments
obj

the ggbrain_images object to combine with this one

Method add_labels()

add a labels data.frame that connects an integer-valued image with a set of labels

Usage
ggbrain_images$add_labels(...)
Arguments
...

named arguments containing data.frame objects for each image to be labeled. The argument name should match the image name to be labeled and the value should be a data.frame containing value and label.

Details

As a result of $add_labels, the $get_slices method will always remap the numeric values for label images to the corresponding text-based labels in the label data. In addition, a new attribute will be returned called "slice_labels" that contains a row for each region represented in each slice.

Method add_images()

add one or more images to this ggbrain_images object

Usage
ggbrain_images$add_images(images = NULL, volumes = NULL)
Arguments
images

a character vector of file names containing NIfTI images to read

volumes

a number indicating the volume within the images to read. At present, this must be a single number – perhaps in the future, it could be a vector so that many timepoints in a 4-D image could be displayed.

Method filter_images()

filters an image based on an expression such as a subsetting operation

Usage
ggbrain_images$filter_images(filter = NULL)
Arguments
filter

a character string or numeric vector of the filter to apply

Details

if expr is a numeric vector, only values in this set will be retained. If a character string expression is used, it should use the variable name 'value' to refer to the numeric values to be filtered, such as 'value > 10'.

Method dim()

return the 3D dimensions of the images contained in this object

Usage
ggbrain_images$dim()

Method get_image_names()

return the names of the images contained in this object

Usage
ggbrain_images$get_image_names()

Method get_images()

return the RNifti objects of one or more images contained in this object

Usage
ggbrain_images$get_images(img_names = NULL, drop = TRUE)
Arguments
img_names

The names of images to return. Use $get_image_names() if you're uncertain about what is available.

drop

If TRUE, a single image is returned as an RNifti object, rather than a single-element list containing that object.

Method get_headers()

return the NIfTI headers for one or more images contained in this object

Usage
ggbrain_images$get_headers(img_names = NULL, drop = TRUE)
Arguments
img_names

The names of images whose header are returned. Use $get_image_names() if you're uncertain about what is available.

drop

If TRUE, a single header is returned as an niftiHeader object, rather than a single-element list containing that object.

Method remove_images()

method for removing one or more images from the ggbrain_images object

Usage
ggbrain_images$remove_images(img_names)
Arguments
img_names

names of images to remove from object

Method winsorize_images()

winsorize the tails of a set of images to pull in extreme values

Usage
ggbrain_images$winsorize_images(img_names, quantiles = c(0.001, 0.999))
Arguments
img_names

The names of images in the ggbrain_images object to be winsorized

quantiles

The lower and upper quantiles used to define the thresholds for winsorizing.

Method na_images()

method to set values less than threshold to NA

Usage
ggbrain_images$na_images(img_names, threshold = NULL)
Arguments
img_names

The names of images in the ggbrain_images object whose values should be set to NA

threshold

The threshold value whose absolute value used to determine which voxels to set to NA. If NULL, use the pvt_zero_tol field (default 1e-6).

Method summary()

print a summary of the ggbrain_images object

Usage
ggbrain_images$summary()

Method get_nz_indices()

return the indices of non-zero voxels

Usage
ggbrain_images$get_nz_indices(img_names = NULL)
Arguments
img_names

The names of images in the ggbrain_images object whose non-zero indices should be looked up

Details

Note that this function looks for non-zero voxels in any of the images specified by img_names.

Method add_slices()

adds one or more slices to the cached slices that will be retrieved by $get_slices() when no slices argument is passed.

Usage
ggbrain_images$add_slices(slices = NULL)
Arguments
slices

a character vector containing one or more slices to be extracted by $get_slices. Uses the syntax "<xyz>=<number>". Example: c("x=10", "y=50%")

Method add_contrasts()

adds one or more contrasts to the cached contrasts that will be retrieved by $get_slices() when no contrasts argument is passed.

Usage
ggbrain_images$add_contrasts(contrasts = NULL)
Arguments
contrasts

a character vector containing one or more contrasts to be extracted by $get_slices. Uses the syntax "<img_name>[subset_expression] + <img_name>".

Method reset_slices()

remove all cached slice settings

Usage
ggbrain_images$reset_slices()

Method get_slices()

get slice data for one or more slices based on their coordinates

Usage
ggbrain_images$get_slices(
  slices = NULL,
  img_names = NULL,
  contrasts = NULL,
  fill_labels = FALSE,
  make_square = TRUE,
  remove_null_space = TRUE
)
Arguments
slices

a vector of slice positions

img_names

a character vector of images contained in the ggbrain_images object to be sliced

contrasts

a named character vector of contrasts to be calculated for each slice

fill_labels

if TRUE, the numeric value of the image will be used for any value that does not have a corresponding label in the labels data.frame. Default: FALSE

make_square

If TRUE, make all images square and of the same size

remove_null_space

If TRUE, remove slices where all values are approximately zero

Details

This function always returns a data.frame where each row represents a slice requested by the user. The $slice_data element is a list-column where each element is itself a list of slice data for a given layer/image (e.g., underlay or overlay) . The $slice_matrix is a list-column where each element is a list of 2-D matrices, one per layer/image. @return a ggbrain_slices object containing the requested slices and contrasts

Method get_slices_inplane()

get_slices_inplane is mostly an internal funciton for getting one or more slices from a given plane

Usage
ggbrain_images$get_slices_inplane(
  imgs = NULL,
  slice_numbers,
  plane,
  drop = FALSE
)
Arguments
imgs

The names of images to slice

slice_numbers

The numbers of slices in the specified plant to grab

plane

The image plane to slice. Must be "coronal", "sagittal", or "axial"

drop

if TRUE, a single slice is returned as a 2D matrix instead of a 3D matrix with a singleton first dimension

Returns

A 3D matrix of slices x dim1 x dim2

Method get_labels()

return a list of data.frames containing labels for a given image

Usage
ggbrain_images$get_labels()
Details

the names of the list correspond directly with the names of the images

Method lookup_slices()

internal function to lookup which slices to display along each axis based on their quantile, xyz coordinate, or ijk coordinate

Usage
ggbrain_images$lookup_slices(slices, ignore_null_space = TRUE)
Arguments
slices

A character vector of coordinates for slices to display

ignore_null_space

If TRUE, any coordinates specified as quantiles (e.g., x = 50%) use the quantiles of only the non-zero slices (ignoring blank sliaces)

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_images$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 class for adding labels to a ggbrain_panel

Description

R6 class for adding labels to a ggbrain_panel

R6 class for adding labels to a ggbrain_panel

Value

a ggbrain_label R6 class containing fields related to ggbrain plot labels

Public fields

addl_args

a named list of additional argument to be passed to geom_text/geom_label at render

Active bindings

data

a data.frame containing labels to be printed on the panel. Must contain dim1, dim2, and label as columns. The dim1 and dim2 columns control where the labels will appear on the panel

image

A character string specifying the image to which these labels pertain

label_column

A character string indicating which data.frame column should be used for drawing labels

min_px

A positive integer indicating the minimum number of pixels present on slice that will generate a label

Methods

Public methods

Method new()

create a new ggbrain_label object

Usage
ggbrain_label$new(
  data = NULL,
  geom = "text",
  image = NULL,
  label_column = NULL,
  min_px = NULL,
  ...
)
Arguments
data

a data.frame containing labels to be printed on the panel. Must contain dim1, dim2, and label as columns. The dim1 and dim2 columns control where the labels will appear on the panel

geom

The geom type to be plotted. Must be "text" or "label", corresponding to geom_text and geom_label, respectively.

image

A string specifying the image to which these labels pertain

label_column

the column in data that should be drawn as labels on the plot

min_px

the minimum number of pixels

...

All other arguments that will be passed directly to geom_text or geom_label such as hjust, size, and color

Method add_to_gg()

add this text layer to an existing ggplot object

Usage
ggbrain_label$add_to_gg(base_gg)
Arguments
base_gg

the ggplot object to which we add the layer

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_label$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 class for a single layer of a ggbrain panel

Description

R6 class for a single layer of a ggbrain panel

R6 class for a single layer of a ggbrain panel

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at geom_brain() and geom_outline().

Value

a ggbrain_layer R6 class containing fields related to a visual layer on the ggbrain plot

Active bindings

name

the name of this layer, used for referencing in layer and panel modifications

all_na

whether all values for this layer are NA in the data field

definition

a character string specifying the image name or contrast that defines this layer

source

a character string specifying the layer source within a relevant ggbrain_slices object. This is used to lookup the right layer information when combining slices and layers together Note that multiple layers can potentially have the same source, which is why a 1:1 mapping to name does not work

data

the data.frame containing relevant data for this layer.

show_legend

a logical indicating whether to show or hide the fill/color scale

unify_scales

a logical indicating whether to unify scale limits and levels when this layer is added across many panels

bisided

read-only access to whether this layer uses a bisided color scale

categorical_fill

read-only access to whether this layer has a categorical fill scale

fill_column

read-only access to layer fill column

fill_scale

a scale_fill_* object containing the ggplot2 fill scale for this layer

alpha

sets the alpha transparency of this layer.

blur_edge

controls the standard deviation (sigma) of a Gaussian blur applied to the layer at the edge

trim_threads

iteratively trim any pixels that have fewer than this number of neighboring pixels

fill_holes

controls the size of holes to be filled for display (in pixels)

remove_specks

controls the size of specks to be removed (in pixels)

Methods

Public methods

Method new()

create a new ggbrain_layer object

Usage
ggbrain_layer$new(
  name = NULL,
  definition = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = NULL,
  unify_scales = TRUE,
  alpha = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  data = NULL
)
Arguments
name

the name of this layer, used for referencing in layer and panel modifications

definition

an optional character string defining the image or contrast that should be used to lookup data from a ggbrain_slices object. This is mostly used internally by the ggbrain + syntax to allow layers to be defined without data in advance of the plot.

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the color scale

show_legend

if TRUE, show the scale on the plot legend

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

fixed alpha transparency of this layer (use mapping for alpha mapping')

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation prior to display

remove_specks

the size of specks (in pixels) to be removed from each slice prior to display

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel

data

the data.frame containing image data for this layer. Must contain "dim1", "dim2", and "value" as columns

Method set_limits()

set the limits for this layer's scale

Usage
ggbrain_layer$set_limits(limits)
Arguments
limits

a 2-element numeric vector setting the lower and upper limits on the layer's scale

Method set_pos_limits()

set the limits for this layer's positive scale (only relevant to bisided)

Usage
ggbrain_layer$set_pos_limits(limits)
Arguments
limits

a 2-element numeric vector setting the lower and upper limits on the layer's positive scale

Method set_neg_limits()

set the limits for this layer's positive scale (only relevant to bisided)

Usage
ggbrain_layer$set_neg_limits(limits)
Arguments
limits

a 2-element numeric vector setting the lower and upper limits on the layer's positive scale

Method set_breaks()

set the breaks element of this layer's scale

Usage
ggbrain_layer$set_breaks(breaks)
Arguments
breaks

a function used to label the breaks

Method set_pos_breaks()

set the breaks element of this layer's positive scale (only relevant to bisided)

Usage
ggbrain_layer$set_pos_breaks(breaks)
Arguments
breaks

a function used to label the positive breaks

Method set_neg_breaks()

set the breaks element of this layer's negative scale (only relevant to bisided)

Usage
ggbrain_layer$set_neg_breaks(breaks)
Arguments
breaks

a function used to label the negative breaks

Method plot()

plot this layer alone (mostly for debugging)

Usage
ggbrain_layer$plot()

Method add_to_gg()

method to add this layer to an existing ggplot object

Usage
ggbrain_layer$add_to_gg(base_gg)
Arguments
base_gg

the ggplot object to which we add the layer

Method get_data()

return the data.frame associated with this layer

Usage
ggbrain_layer$get_data(add_layer_name = FALSE)
Arguments
add_layer_name

if TRUE, adds a layer_name column to the data.frame for record-keeping. Default: FALSE.

Method is_empty()

returns TRUE if all values are NA or if the data has 0 rows

Usage
ggbrain_layer$is_empty()

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_layer$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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

Description

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

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

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at geom_brain().

Value

a ggbrain_layer_brain R6 class with fields related to a brain visual layer (relates to geom_brain)

Super class

ggbrain::ggbrain_layer -> ggbrain_layer_brain

Active bindings

fill

controls color of the filled in pixels for non-NA (valid) voxels. Note that this sets the fill color, while the mapping=aes(fill=<value>) would map the fill to a column in the data, consistent with ggplot2 logic.

mapping

the ggplot2 aesthetic mapping between the data columns and the display

Methods

Public methods

Inherited methods

Method new()

create a new ggbrain_layer object

Usage
ggbrain_layer_brain$new(
  name = NULL,
  definition = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = NULL,
  unify_scales = TRUE,
  alpha = NULL,
  mapping = ggplot2::aes(fill = value),
  fill = NULL,
  fill_scale = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  data = NULL
)
Arguments
name

the name of this layer, used for referencing in layer and panel modifications

definition

an optional character string defining the image or contrast that should be used to lookup data from a ggbrain_slices object. This is mostly used internally by the ggbrain + syntax to allow layers to be defined without data in advance of the plot.

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the color scale

show_legend

if TRUE, show the scale on the plot legend

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

a number between 0 and 1 that sets the alpha transparency of this layer. Default: 1

mapping

the aesthetic mapping of the layer data to the display. Should be an aes() object and supports fill (color of filled pixels). Default is aes(fill=value), which maps the numeric value of the layer data to the fill color of the squares at each spatial position. For labeled data, you might use aes(fill=<label_col_name>).

fill

A character string indicating the color used to fill all non-NA pixels in this layer. This is used in distinction to mapping=aes(fill=<variable>).

fill_scale

a ggplot scale object used for mapping the value column as the fill color for the layer.

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation prior to display

remove_specks

the size of specks (in pixels) to be removed from each slice prior to display

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel

data

the data.frame containing image data for this layer. Must contain "dim1", "dim2", and "value" as columns

Details

To set mapping, you must provide a ggplot2 aes() object. A geom_brain() layer requires a fill aesthetic mapping, which controls the fill color of regions.

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_layer_brain$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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

Description

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

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

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at geom_outline().

Value

a ggbrain_layer_outline R6 class with fields related to a brain visual layer (relates to geom_outline)

Super class

ggbrain::ggbrain_layer -> ggbrain_layer_outline

Active bindings

mapping

the ggplot2 aesthetic mapping between the data columns and the display

outline

controls color of outline draw around non-NA (valid) voxels

outline_scale

a scale_fill_* object containing the ggplot2 outline color scale for this layer

size

controls size of outline drawn around non-NA (valid) voxels

dil_ero

controls the number of pixels to dilate (> 0) or erode (< 0) the outline

Methods

Public methods

Inherited methods

Method new()

create a new ggbrain_layer object

Usage
ggbrain_layer_outline$new(
  name = NULL,
  definition = NULL,
  limits = NULL,
  breaks = integer_breaks(),
  show_legend = TRUE,
  interpolate = NULL,
  unify_scales = TRUE,
  alpha = NULL,
  mapping = ggplot2::aes(outline = NULL, fill = NULL),
  outline = NULL,
  outline_scale = NULL,
  size = NULL,
  blur_edge = NULL,
  fill_holes = NULL,
  remove_specks = NULL,
  trim_threads = NULL,
  dil_ero = NULL,
  data = NULL
)
Arguments
name

the name of this layer, used for referencing in layer and panel modifications

definition

an optional character string defining the image or contrast that should be used to lookup data from a ggbrain_slices object. This is mostly used internally by the ggbrain + syntax to allow layers to be defined without data in advance of the plot.

limits

if provided, sets the upper and lower bounds on the scale

breaks

if provided, a function to draw the breaks on the color scale

show_legend

if TRUE, show the scale on the plot legend

interpolate

passes to geom_raster and controls whether the fill is interpolated over continuous space

unify_scales

if TRUE, when this layer is reused across panels, unify the scales to match

alpha

a number between 0 and 1 that sets the alpha transparency of this layer. Default: 1

mapping

the aesthetic mapping of the layer data to the display. Should be an aes() object and supports outline (color of outline around clusters). Default is aes(outline=value), which maps the numeric value of the layer data to the outline color of the squares at around spatial regions. For labeled data, you might use aes(fill=<label_col_name>).

outline

A character string indicating the color used to outline all non-NA pixels in this layer. This is used in distinction to mapping=aes(outline=<variable>).

outline_scale

a ggplot scale object used for mapping the value column as the outline color for the layer.

size

controls the thickness of outlines

blur_edge

the standard deviation (sigma) of a Gaussian kernel applied to the edge of this layer to smooth it. This makes the layer less jagged in appearance and is akin to antialiasing.

fill_holes

the size of holes (in pixels) inside clusters to be filled by nearest neighbor imputation prior to display

remove_specks

the size of specks (in pixels) to be removed from each slice prior to display

trim_threads

the minimum number of neighboring pixels (including diagonals) that must be present to keep a pixel

dil_ero

the number of pixels to dilate (> 0) or erode (<0) the outline.

data

the data.frame containing image data for this layer. Must contain "dim1", "dim2", and "value" as columns

Details

To set mapping, you must provide a ggplot2 aes() object. A geom_outline() layer requires an outline aesthetic mapping, which controls the color of outlines drawn around regions.

note that the ggbrain_layer_outline class maps onto *_fill fields

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_layer_outline$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 class for a single panel of a ggbrain image

Description

R6 class for a single panel of a ggbrain image

R6 class for a single panel of a ggbrain image

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at slices().

Value

a ggbrain_panel R6 class with fields related to a panel on the ggbrain plot

Public fields

gg

The ggplot object that contains the panel

Methods

Public methods

Method new()

create a new ggbrain_panel object

Usage
ggbrain_panel$new(
  layers = NULL,
  title = NULL,
  bg_color = NULL,
  text_color = NULL,
  border_color = NULL,
  border_size = NULL,
  xlab = NULL,
  ylab = NULL,
  theme_custom = NULL,
  annotations = NULL,
  region_labels = NULL
)
Arguments
layers

a list of ggbrain_layer objects to form the panel

title

a title for the panel added to the ggplot object using ggtitle()

bg_color

the color used for the background of the plot. Default: 'gray10' (nearly black)

text_color

the color used for text displayed on the plot. Default: 'white'.

border_color

the color used for drawing a border around on the plot. Default: 'gray50' (though borders are not drawn by default).

border_size

the size of the border line drawn around the panel. Default: NULL. If this value is greater than zero, a border of this size and with color border_color will be drawn around the panel

xlab

The label to place on x axis. Default is NULL.

ylab

The label to place on y axis. Default is NULL.

theme_custom

Any custom theme() settings to be added to the plot

annotations

a data.frame containing all annotations to be added to this plot. Each row is cleaned up and passed to ggplot2::annotate()

region_labels

a list of ggbrain_label objects with data for plotting region labels on this panel

Method reset_limits()

Reset the scale limits for the specified layers

Usage
ggbrain_panel$reset_limits(layer_names)
Arguments
layer_names

not implemented yet

Method plot()

plot the panel

Usage
ggbrain_panel$plot(use_global_limits = TRUE)
Arguments
use_global_limits

Not implemented at present

Method add_to_gg()

add one or more custom ggplot settings to the panel

Usage
ggbrain_panel$add_to_gg(list_args)
Arguments
list_args

A list containing elements to add to the ggplot object

Details

Note that passing in an expression such as theme_bw() + ggtitle("hello") will not work because it creates an object that cannot be added sequentially to the ggplot. As noted in ggplot2's documentation (https://ggplot2.tidyverse.org/reference/gg-add.html), to programmatically add elements to a ggplot, pass in a list where each element is added sequentially

Method add_layer()

adds a ggplot_layer object to the panel

Usage
ggbrain_panel$add_layer(layer_obj)
Arguments
layer_obj

a ggbrain_layer object to add to the panel

Method remove_layers()

removes one or more layers by name

Usage
ggbrain_panel$remove_layers(layer_names)
Arguments
layer_names

a character string of the layers to remove from the panel

Method get_data()

returns the data for all layers in the object

Usage
ggbrain_panel$get_data()

Method get_layer_names()

returns the names of the layers in this panel, ordered from bottom to top

Usage
ggbrain_panel$get_layer_names()

Method get_layers()

returns a list of ggbrain_layer objects that comprise this panel

Usage
ggbrain_panel$get_layers()

Method set_layer_order()

sets the order of layers from bottom to top based on the layer names provided

Usage
ggbrain_panel$set_layer_order(ordered_names = NULL)
Arguments
ordered_names

the names of the layers in the desired order from bottom to top. All layer names must be provided, not just a subset

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_panel$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

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

Description

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

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

Details

Note that this class is exported only for power users and rarely needs to be called directly in typical use of the package. Instead, look at ggbrain().

Value

a ggbrain_plot R6 class containing fields related to a ggbrain plot object

Active bindings

slices

a ggbrain_slices object containing all slice data for this plot

layers

a list of ggbrain_layer objects for this plot. Note that in assignment, the input can be a list of ggbrain_layer objects, or a list of lists where each inner element specifies the settings for that layer. Example: ⁠list(list(name='hello', fill_scale=scale_fill_distiller())⁠

annotations

a list of annotations to be added to this plot

region_labels

a list of region_labels to be added to this plot

panel_settings

a list of panel settings (aesthetics) to be added to this plot

title

overall plot title, added to composite plot by patchwork::plot_annotation()

bg_color

background color of plot

text_color

the color of text use across panels (can be overridden by panel settings)

base_size

the base size of text used in ggplot theming

Methods

Public methods

Method new()

instantiate a new instance of a ggbrain_plot object

Usage
ggbrain_plot$new(
  title = NULL,
  bg_color = NULL,
  text_color = NULL,
  base_size = NULL,
  slice_data = NULL
)
Arguments
title

overall plot title

bg_color

background color of plot

text_color

text color of plot

base_size

base size of text used in ggplot theming

slice_data

a ggbrain_slices object generated by ggbrain_images$get_slices()

Method add_layers()

adds one or more ggbrain_layer objects to this plot

Usage
ggbrain_plot$add_layers(layers = NULL)
Arguments
layers

a list of ggbrain_layer objects (can also be a list that just specifies names, definitions, etc.)

Method reset_layers()

removes all existing layers from this ggbrain_plot object

Usage
ggbrain_plot$reset_layers()

Method generate_plot()

generate the plot

Usage
ggbrain_plot$generate_plot(layers = NULL, slice_indices = NULL)
Arguments
layers

a list of layers to be displayed on each panel, the order of which yields the bottom-to-to drawing order within ggplot2. Each element of layers should be a list that follows the approximate structure of the ggbrain_layer class, minimally including the layer name, which is used to lookup data of images or contrasts within the slice_data object. If NULL, all layers in the slices object will be plotted. If only a character string is passed, then those layers will be plotted with default scales.

slice_indices

An optional subset of slice indices to display from the stored slice data

Details

In addition to name, the elements of a layer can include fill_scale a ggplot2 scale object for coloring the layer. Should be a scale_fill_* object. limits the numeric limits to use for the color scale of this layer breaks the scale breaks to use for the color scale of this layer show_legend if FALSE, the color scale will not appear in the legend

Method plot()

return a plot of all panels as a patchwork object

Usage
ggbrain_plot$plot(guides = "collect", ...)
Arguments
guides

Passes through to patchwork::plot_layout to control how legends are combined across plots. The default is "collect", which collects legends within a given nesting level (removes duplicates).

...

additional arguments. Not used currently

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_plot$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

R6 class for managing slice data for ggbrain plots

Description

R6 class for managing slice data for ggbrain plots

R6 class for managing slice data for ggbrain plots

Active bindings

slice_index

read-only access to the slice_index containing the slice numbers

coord_input

the input string used to lookup the slices

coord_label

the calculated x, y, or z coordinate of the relevant slice

slice_number

the slice number along the relevant axis of the 3D image matrix

slice_data

a nested list of data.frames where each element contains all data relevant to that slice and the list elements within are each a given image

slice_matrix

the slice data in matrix form

slice_labels

a data.frame for each slice containing the coordinates of labels available to be drawn

layer_names

a character vector of layer names within each slice

Methods

Public methods

Method new()

create a ggbrain_slices object based

Usage
ggbrain_slices$new(slice_df = NULL)
Arguments
slice_df

a data.frame generated by ggbrain_images$get_slices()

Details

If this becomes a user-facing/exported class, we may want a more friendly constructor

Method compute_contrasts()

computes contrasts of the sliced image data

Usage
ggbrain_slices$compute_contrasts(contrast_list = NULL)
Arguments
contrast_list

a named list or character vector containing contrasts to be computed. The names of the list form the contrast names, while the values should be character strings that use standard R syntax for logical tests, subsetting, and arithmetic

Method as_tibble()

convert the slices object into a data.frame with list-columns for slice data elements

Usage
ggbrain_slices$as_tibble()

Method get_ranges()

calculates the numeric ranges of each image/contrast in this object, across all constituent slices. This is useful for setting scale limits that are shared across panels

Usage
ggbrain_slices$get_ranges(slice_indices = NULL)
Arguments
slice_indices

an optional integer vector of slice indices to be used as a subset in the calculation

Returns

a tibble keyed by 'layer' with overall low and high values, as well as split by pos/neg

Method get_uvals()

returns a data.frame with the unique values for each label layer, across all constituent slices

Usage
ggbrain_slices$get_uvals(slice_indices = NULL, add_labels = NULL)
Arguments
slice_indices

an optional integer vector of slice indices to be used as a subset in the calculation

add_labels

an optional named list indicating the label columns to add to a given layer. The names of the list specify the layer to which labels are added and the values should be character vectors specifying the names of columns that serve as labels for the layer. These are always added to any existing label columns for the layer.

Details

add_labels is provided here for any categorical columns that were specified inline in the layer definition using factor or as.factor, such as aes(fill=factor(value)). Otherwise, it's best to input data with labels in the first place so that labels are described in the data structure itself.

Method clone()

The objects of this class are cloneable with this method.

Usage
ggbrain_slices$clone(deep = FALSE)
Arguments
deep

Whether to make a deep clone.

Author(s)

Michael Hallquist

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

Description

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

Usage

## S3 method for class 'ggbrain_label'
ggplot_add(object, plot, object_name)

Arguments

object

the ggbrain_layer object to be added to an existing ggplot

plot

the ggplot object

object_name

not used, but required by ggplot_add

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

Description

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

Usage

## S3 method for class 'ggbrain_layer'
ggplot_add(object, plot, object_name)

Arguments

object

the ggbrain_layer object to be added to an existing ggplot

plot

the ggplot object

object_name

not used, but required by ggplot_add

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

Description

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

Usage

## S3 method for class 'ggbrain_panel'
ggplot_add(object, plot, object_name)

Arguments

object

the ggbrain_layer object to be added to an existing ggplot

plot

the ggplot object

object_name

not used, but required by ggplot_add

Add images to a ggbrain object

Description

Add images to a ggbrain object

Usage

images(images = NULL, volumes = NULL, labels = NULL, filter = NULL)

Arguments

images

a character vector or ggbrain_images object containing NIfTI images to add to this plot

volumes

a number indicating the volume within the images to display. At present, this must be a single number – perhaps in the future, it could be a vector so that many timepoints in a 4-D image could be displayed.

labels

a data.frame or named list of data.frame objects corresponding to images that should be labeled. You can only provide a data.frame if there is a single image being added. If multiple images are added, the names of the labels list are used to align the labels with a given matching image.

filter

a named list or character string specifying an expression of values to retain in the image, or a numeric vector of values to retain. Calls ggbrain_images$filter_image()

Value

a ggb object with the relevant images and an action of 'add_images'

Examples

  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")
  gg_obj <- ggbrain() +
    images(c(underlay = t1))

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

Description

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

Usage

integer_breaks(n = 5, ...)

Arguments

n

number of breaks (default = 5)

...

Additional arguments passed to the pretty() function

Details

Code from here: https://joshuacook.netlify.app/post/integer-values-ggplot-axis/

Value

a function for generating integer-valued breaks on a continuous scale

Finds the mode of an integer vector

Description

Finds the mode of an integer vector

Arguments

v

a vector of integers

demote_zeros

if TRUE, zero will not be allowed to be the mode

Value

An integer representing the mode of the vector. If multiple modes are found, then the lowest-valued mode is returned

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

Description

Converts a 2D numeric matrix into a 3-column data.frame

Arguments

mat

A matrix to convert to data.frame

Details

This function is a faster version of reshape2::melt for the simple 2-D case. It is about 2.5x faster than melt.

Value

A 3-column data.frame with dim1, dim2, and value

Author(s)

Michael Hallquist

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

Description

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

Usage

montage(
  plane = NULL,
  n = 12,
  min = 0.1,
  max = 0.9,
  min_coord = NULL,
  max_coord = NULL
)

Arguments

plane

a character string specifying the 3D plane: "sagittal", "axial", "coronal", "x", "y", or "z"

n

number of slices to add in this plane. Default: 12

min

the lowest quantile to be included in the montage (between 0 and 1). Default: 0.1

max

the highest quantile to be included in the montage (between 0 and 1). Default: 0.9

min_coord

the lowest spatial position (in image coordinate space) to be included in the montage.

max_coord

the highest spatial position (in image coordinate space) to be included in the montage.

Details

This can be used with slices to make a quick montage, such as ⁠slices(montage("axial", 10)⁠.

Also note that use of standardized coordinates (in quantiles, using min and max) is mutually exclusive with the the image coordinate specifications min_coord and max_coord.

Value

a character string containing the slice positions along the requested axis

Examples

  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")
  gg_obj <- ggbrain() +
    images(c(underlay = t1)) +
    slices(montage("sagittal", 15))

little helper function to create named list from objects

Description

little helper function to create named list from objects

Usage

named_list(...)

Arguments

...

A set of arguments to be compiled into a list

Details

The names of the objects will form the names of the list elements

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

Description

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

Arguments

x

x-position of the point whose neighbors should be found within in_mat

y

y-position of the point whose neighbors should be found within in_mat

in_mat

a 2D matrix to search for neighbors of pt

neighbors

the number of closest non-NA neighboring values to return within in_mat

radius

the radius around pt to search. Default: 8.

ignore_zeros

if TRUE, then zero is not a valid imputation value (since these are not data in NIfTIs)

Value

A vector of neighbors closest neighboring values around pt

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

Description

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

Arguments

in_mat

a 2D matrix to fill using nearest neighbors

neighbors

the number of closest non-NA neighboring values to return within in_mat. Default is 4.

radius

the radius (in pixels) around each missing value to search for non-missing neighbors. Default is 8.

aggfun

the function used to aggregate the neighbors in imputation. Supports "mean", "median", and "mode."

ignore_zeros

if TRUE, then zero is not a valid imputation value (since these are not data in NIfTIs)

Details

The "mode" aggfun should only be used when the matrix in_mat can be converted to integers without loss of information (i.e., the data are integerish values already).

Value

A copy of the matrix with NA values imputed by their nearest neighbors

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

Description

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

Usage

## S3 method for class 'ggb'
plot(x, ...)

Arguments

x

the ggb object to be plotted

...

additional arguments passed to the plot method

Details

This will plot the ggbrain object to the current graphics device

Value

NULL, invisibly

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

Description

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

Usage

## S3 method for class 'ggbrain_panel'
plot(x, ...)

Arguments

x

the ggbrain_panel object to be plotted

...

additional argument passed to the plot method

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

Description

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

default S3 method for ggbrain_patchwork objects (post-render)

Usage

## S3 method for class 'ggbrain_patchwork'
plot(x, ...)

## S3 method for class 'ggbrain_patchwork'
print(x, ...)

Arguments

x

the ggbrain_patchwork object to be plotted

...

additional arguments. Not currently used

Value

patchworkGrob object, invisibly

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

Description

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

Usage

## S3 method for class 'ggbrain_plot'
plot(x, ...)

Arguments

x

the ggbrain_plot object to be plotted

...

additional argument passed to the plot method

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

Description

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

Usage

range_breaks(n = 3, digits = 2)

Arguments

n

number of breaks added within the min-max range

digits

number of decimal places to display

Value

a function for generating breaks on a continuous scale with the min and max labeled

Function to convert ggb object to ggplot/patchwork object

Description

Function to convert ggb object to ggplot/patchwork object

Usage

render(x, ...)

Arguments

x

optional. A ggb object to be rendered into a ⁠ggbrain_patchwork object⁠.

...

additional arguments passed to the $render method of x.

Details

If no x argument is passed in, this function can be used in a ggbrain addition chain to render a plot to a ggplot-friendly object before additional ggplot or patchwork calls are added such as theme().

Or if x is passed in as an argument, return the rendered plot as a ggbrain_patchwork object.

Value

a ggbrain_patchwork object of the rendered ggbrain plot

Examples

  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")
  
  # version where render is added to the object in a ggplot-style chain
  gg_obj <- ggbrain() +
    images(c(underlay = t1)) + 
    slices(c("x = 25%", "x = 75%")) +
    geom_brain("underlay") + 
    render() + # convert to ggplot-friendly object
    ggplot2::theme(text=ggplot2::element_text(family="Serif"))
    
 # version where a ggbrain object is created in one step, then rendered in another
 brain_obj <- ggbrain() +
    images(c(underlay = t1)) + 
    slices(c("x = 25%", "x = 75%")) +
    geom_brain("underlay")
    
 gg_obj <- render(brain_obj) + patchwork::plot_annotation(title="Overall title")

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

Description

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

Usage

## S3 method for class 'ggb'
render(x, ...)

Arguments

x

the ggb object to be rendered to a ggbrain_patchwork object

...

additional arguments passed to the render method

Value

the ggbrain_patchwork object that can be handed off to patchwork and ggplot2 functions.

scale for plotting separate color gradients for positive and negative values

Description

scale for plotting separate color gradients for positive and negative values

Usage

scale_fill_bisided(
  name = ggplot2::waiver(),
  neg_scale = scale_fill_distiller(palette = "Blues", direction = 1),
  pos_scale = scale_fill_distiller(palette = "Reds"),
  symmetric = TRUE
)

Arguments

name

the scale name to be printed in the legend (above positive scale)

neg_scale

a scale_fill_* object used for negative values

pos_scale

a scale_fill_* object used for positive values

symmetric

if TRUE, the limits of the positive scale will equal the inverse limits of the negative scale. Said differently, this makes the positive and negative scales symmetric

Details

Note that this will absolutely not work as a general purpose ggplot2 scale! The positive/negative combination is achieved by adding two layers/geoms behind the scenes with different color scale.

Value

a ggplot2 scale of type ScaleContinuous that includes negative and positive fill scales internally in the ⁠$neg_scale⁠ and ⁠$pos_scale⁠ elements

Adds slices to the ggbrain plot, including additional panel aesthetics

Description

Adds slices to the ggbrain plot, including additional panel aesthetics

Usage

slices(
  coordinates = NULL,
  title = NULL,
  bg_color = NULL,
  text_color = NULL,
  border_color = NULL,
  border_size = NULL,
  xlab = NULL,
  ylab = NULL,
  theme_custom = NULL
)

Arguments

coordinates

a character vector specifying the x, y, or z coordinates of the slices to be added.

title

a title for the slice panels added to the ggplot object using ggtitle()

bg_color

the color used for the background of the panels. Default: 'gray10' (nearly black)

text_color

the color used for text displayed on the panels. Default: 'white'.

border_color

the color used for drawing a border around on the panels. Default: 'gray50' (though borders are not drawn by default).

border_size

the size of the border line drawn around the panels. Default: NULL. If this value is greater than zero, a border of this size and with color border_color will be drawn around the panels.

xlab

The label to place on x axis. Default is NULL.

ylab

The label to place on y axis. Default is NULL.

theme_custom

Any custom theme() settings to be added to the panels.

Details

note that if you pass in multiple coordinates (as a vector), the title, bg_color, and other attributes will be reused for all slices added by this operation. Thus, if you want to customize specific slices or groups of slices, use multiple addition operations, as in slices(c('x=10', 'y=15'), bg_color='white') + slices(c('x=18', 'y=22'), bg_color='black').

Value

a ggb object with the relevant slices and an action of 'add_slices'

Examples

  t1 <- system.file("extdata", "mni_template_2009c_2mm.nii.gz", package = "ggbrain")
  gg_obj <- ggbrain() +
    images(c(underlay = t1)) +
    slices(c("x = 25%", "x = 75%"), border_color = "blue")

Sort Matrix by Column

Description

Sorts a given matrix by a specific column while retain the elements in each row.

Arguments

x

A matrix to sort

col

A int that indicates the column the matrix should sort by.

Details

This functions sorts a matrix based on one column, keeping the rows together. Note that col should be a zero-based index of x (i.e., first column is 0).

Value

The matrix sorted by values in the specified column.