topoplot: Topographical Plotting Function for EEG

In neuroconductor-devel-releases/eegUtils: A collection of utilities for EEG analysis

Description

Allows topographical plotting of functional data. Output is a ggplot2 object.

Usage

topoplot(data, ...)

## Default S3 method:
topoplot(data, ...)

## S3 method for class 'data.frame'
topoplot(data, time_lim = NULL, limits = NULL,
  chanLocs = NULL, method = "Biharmonic", r = NULL, grid_res = 67,
  palette = "RdBu", interp_limit = "skirt", contour = TRUE,
  chan_marker = "point", quantity = "amplitude", montage = NULL,
  colourmap, highlights = NULL, scaling = 1, groups = NULL, ...)

## S3 method for class 'eeg_data'
topoplot(data, time_lim = NULL, limits = NULL,
  chanLocs = NULL, method = "Biharmonic", r = NULL, grid_res = 67,
  palette = "RdBu", interp_limit = "skirt", contour = TRUE,
  chan_marker = "point", quantity = "amplitude", montage = NULL,
  highlights = NULL, scaling = 1, ...)

## S3 method for class 'eeg_epochs'
topoplot(data, time_lim = NULL, limits = NULL,
  chanLocs = NULL, method = "Biharmonic", r = NULL, grid_res = 67,
  palette = "RdBu", interp_limit = "skirt", contour = TRUE,
  chan_marker = "point", quantity = "amplitude", montage = NULL,
  highlights = NULL, scaling = 1, groups = NULL, ...)

## S3 method for class 'eeg_ICA'
topoplot(data, component, time_lim = NULL,
  limits = NULL, chanLocs = NULL, method = "Biharmonic", r = NULL,
  grid_res = 67, palette = "RdBu", interp_limit = "skirt",
  contour = TRUE, chan_marker = "point", quantity = "amplitude",
  montage = NULL, colourmap, highlights = NULL, scaling = scaling,
  ...)

## S3 method for class 'eeg_tfr'
topoplot(data, time_lim = NULL, limits = NULL,
  chanLocs = NULL, method = "Biharmonic", r = NULL, grid_res = 67,
  palette = "RdBu", interp_limit = "skirt", contour = TRUE,
  chan_marker = "point", quantity = "power", montage = NULL,
  highlights = NULL, scaling = 1, freq_range = NULL, ...)

Arguments

data	An EEG dataset. If the input is a data.frame, then it must have columns x, y, and amplitude at present. x and y are (Cartesian) electrode co-ordinates), amplitude is amplitude.
...	Various arguments passed to specific functions
time_lim	Timepoint(s) to plot. Can be one time or a range to average over. If none is supplied, the function will average across all timepoints in the supplied data.
limits	Limits of the fill scale - should be given as a character vector with two values specifying the start and endpoints e.g. limits = c(-2,-2). Will ignore anything else. Defaults to the range of the data.
chanLocs	Allows passing of channel locations (see electrode_locations)
method	Interpolation method. "Biharmonic" or "gam". "Biharmonic" implements the same method used in Matlab's EEGLAB. "gam" fits a Generalized Additive Model with k = 40 knots. Defaults to biharmonic spline interpolation.
r	Radius of cartoon head_shape; if not given, defaults to 1.1 * the maximum y electrode location.
grid_res	Resolution of the interpolated grid. Higher = smoother but slower.
palette	Defaults to RdBu if none supplied. Can be any from RColorBrewer or viridis. If an unsupported palette is specified, switches to Greens.
interp_limit	"skirt" or "head". Defaults to "skirt". "skirt" interpolates just past the farthest electrode and does not respect the boundary of the head_shape. "head" interpolates up to the radius of the plotted head.
contour	Plot contour lines on topography (defaults to TRUE)
chan_marker	Set marker for electrode locations. "point" = point, "name" = electrode name, "none" = no marker. Defaults to "point".
quantity	Allows plotting of arbitrary quantitative column. Defaults to amplitude. Use quoted column names. E.g. "p.value", "t_statistic".
montage	Name of an existing montage set. Defaults to NULL; (currently only 'biosemi64alpha' available other than default 10/20 system)
colourmap	Deprecated, use palette instead.
highlights	Electrodes to highlight (in white)
scaling	Scaling multiplication factor for labels and any plot lines. Defaults to 1.
groups	Column name for groups to retain.
component	Component to plot (numeric)
freq_range	Range of frequencies to average over.

Methods (by class)

• default: Default method for data frames.

• data.frame: Topographical plotting of data.frames and other non eeg_data objects.

• eeg_data: Topographical plotting of eeg_data objects.

• eeg_epochs: Topographical plotting of eeg_epochs objects.

• eeg_ICA: Topographical plot for eeg_ICA objects

• eeg_tfr: Topographical plotting of eeg_tfr objects.

Notes on usage of Generalized Additive Models for interpolation

The function fits a GAM using the gam function from mgcv. Specifically, it fits a spline using the model function gam(z ~ s(x, y, bs = "ts", k = 40). Using GAMs for smooths is very much experimental. The surface is produced from the predictions of the GAM model fitted to the supplied data. Values at each electrode do not necessarily match actual values in the data: high-frequency variation will tend to be smoothed out. Thus, the method should be used with caution.

Author(s)

Matt Craddock, [e-mail]

neuroconductor-devel-releases/eegUtils documentation built on May 5, 2020, 3:49 a.m.