ggbrain (version 0.9.0)

geom_outline: 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
)

Value

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

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.

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")