plot_topo: Visualization of EEG topo maps.
In itsadug: Interpreting Time Series and Autocorrelated Data Using GAMMs

plot_topo

R Documentation

Visualization of EEG topo maps.

Description

Visualization of EEG topo maps.

Usage

plot_topo(
  model,
  view,
  el.pos = NULL,
  fun = "fvisgam",
  add.color.legend = TRUE,
  size = 5,
  n.grid = 100,
  col = 1,
  pch = 21,
  bg = alpha(1),
  color = "bwr",
  xlab = "",
  ylab = "",
  setmargins = TRUE,
  ...
)

Arguments

`model`	A gam object, produced by `gam` or `bam`.
`view`	A two-value vector containing the names of the two main effect terms to be displayed on the x and y dimensions of the plot. Note that variables coerced to factors in the model formula won't work as view variables.
`el.pos`	A list with X and Y positions and Electrodes, which are used for fitting the model.
`fun`	Text string, 'fvisgam', 'pvisgam', or 'plot_diff2' signalling which function to use for plotting.
`add.color.legend`	Logical: whether or not to add a color legend. Default is TRUE. If FALSE (omitted), one could use the function `gradientLegend` to add a legend manually at any position.
`size`	Size in inch of plot window.
`n.grid`	The number of grid nodes in each direction used for calculating the plotted surface.
`col`	The colors for the background of the plot.
`pch`	The type of points as indications for the electrode positions. The value NA will suppress the plotting of electrode positions.
`bg`	The background color of the points.
`color`	The color scheme to use for plots. One of 'topo', 'heat', 'cm', 'terrain', 'gray', 'bw', or 'rwb' (red-white-blue; default).
`xlab`	Label x-axis. Default excluded.
`ylab`	Label y-axis. Default excluded.
`setmargins`	Logical: whether or not to automatically set the margins. By default set to TRUE. If set to false, the size can
`...`	other options to pass on to `fvisgam`, `pvisgam`, or `plot_diff2`.

Notes

X-positions of electrodes should have lower values for electrodes on the left hemisphere (e.g. T7) than for electrodes on the right hemisphere. Y-positions of electrodes should have lower values for electrodes at the back of the head than for the frontal electrodes.

Author(s)

Jacolien van Rij

Examples


data(eeg)

## Not run: 
# simple GAMM model:
m1 <- gam(Ampl ~ te(Time, X, Y, k=c(10,5,5), 
    d=c(1,2)), data=eeg)

# topo plot, by default uses fvisgam 
# and automatically selects a timestamp (270ms):
plot_topo(m1, view=c('X', 'Y'))
# or:
plot_topo(m1, view=c('X', 'Y'), setmargins=FALSE, size=1)

# add electrodes:
electrodes <- eeg[,c('X','Y','Electrode')]
electrodes <- as.list( electrodes[!duplicated(electrodes),] )
plot_topo(m1, view=c('X', 'Y'), el.pos=electrodes)

# some formatting options:
plot_topo(m1, view=c('X', 'Y'), el.pos=electrodes,
    main='Topo plot', zlim=c(-.5,.5), 
    pch=15, col='red', color='terrain')

# plotting more than one panel only works if 
# each figure region is a square:
dev.new(width=12, height=4) 
par(mfrow=c(1,3))

for(i in c(100, 200, 300)){
    # make sure to keep zlim constant:
\t   plot_topo(m1, view=c('X', 'Y'), zlim=c(-.5, .5), 
    cond=list(Time=i), el.pos=electrodes,
    main=i)
}

dev.new(width=12, height=4) 
par(mfrow=c(1,3), cex=1.1)
# The three different functions for plotting:
plot_topo(m1, view=c('X', 'Y'), zlim=c(-.5, .5), 
    el.pos=electrodes,
    fun='fvisgam', main='fvisgam', 
    cond=list(Time=200), rm.ranef=TRUE)
plot_topo(m1, view=c('X', 'Y'), zlim=c(-.5, .5), 
    el.pos=electrodes, select=1,
    fun='pvisgam', main='pvisgam', 
    cond=list(Time=200))
plot_topo(m1, view=c('X', 'Y'), zlim=c(-.5, .5), 
    el.pos=electrodes, comp=list(Time=c(300,100)),
    fun='plot_diff2', main='plot_diff2', 
    plotCI=TRUE)

# Add labels:
plot_topo(m1, view=c('X', 'Y'), zlim=c(-.5, .5), 
    fun='fvisgam', main='', 
    cond=list(Time=200), add.color.legend=FALSE)
text(electrodes[['X']], electrodes[['Y']], 
    labels=electrodes[['Electrode']], cex=.75, 
    xpd=TRUE)

## End(Not run)

itsadug documentation built on June 17, 2022, 5:05 p.m.