plot_topo {itsadug}

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

See Also

Other Functions for model inspection: dispersion(), fvisgam(), gamtabs(), inspect_random(), plot_data(), plot_parametric(), plot_smooth(), pvisgam()

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)