jpsth: Related Functions and Methods for Joint-PSTHs and Joint...

Description Usage Arguments Details Value Note Author(s) References See Also Examples

Description

Some mainly graphical tools to probe interactions between 2 neurons recorded in the presence of a repeated stimulation.

Usage

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jsd(xRT, yRT, acquisitionWindow, xlab, ylab,
    main, pch = ".", ...)
jpsth(xRT, yRT, xBreaks, yBreaks,
      acquisitionWindow, nbEvtPerBin = 50)
## S3 method for class 'jpsth'
contour(x, xlab, ylab, main, ...)
## S3 method for class 'jpsth'
image(x, xlab, ylab, main, ...)
## S3 method for class 'jpsth'
persp(x, xlab, ylab, main, ...)
jpsth2df(object)

Arguments

xRT

a repeatedTrain object whose spike times will appear on the abscissa of the plots.

yRT

a repeatedTrain object whose spike times will appear on the ordinate of the plots. It must have the same length as xRT.

x, object

jpsth objects.

xBreaks, yBreaks

A single number (the bin width) or a vector defining bins boundaries on the X and Y axis. If missing a default is provided.

acquisitionWindow

a 2 elements vector specifying the begining and the end of the acquisition. If missing values are obtained using the floor of the smallest spike time and the ceiling of the largest one.

nbEvtPerBin

If both xBreaks and xBreaks are missing a bin width, bw, is computed such that the expected value of the count per cell (2 dimensional bin) would be nbEvtPerBin assuming a stationary Poisson discharge for both neurons.

xlab

a character (default value supplied). See plot.

ylab

a character (default value supplied). See plot.

main

a character (default value supplied). See plot.

pch

the type of "points" displayed by jsd. See plot.

...

additional arguments passed to plot by jsd and to respective generic methods by contour.jpsth, image.jpsth and persp.jpsth.

Details

The joint scatter diagram was introduced by Gerstein and Perkel (1972). The joint peristimulus time histogram is a binned version of it (Aertsen et al, 1989). jpsth2df allows the reformating of a jpsth object in order to compute a smooth version of it with gam.

Value

jsd is used for its side effect, a plot is generated and nothing is returned.

jpsth2df returns a data.frame with the following variables: Count, the counts per cell; X, the position of the cell on the X axis; Y, the position of the cell on the Y axis; and attributes: xBreaks, yBreaks, xTotal, yTotal, nbTrials, acquisitionWindow corresponding to the components of its argument with the same name and originalCall corresponding to component call.

jpsth returns a list of class jpsth with the following components:

counts

a matrix storing the counts per cell.

density

a matrix storing the density in each cell.

xMids

a vector containing the X positions of the cells.

yMids

a vector containing the Y positions of the cells.

xBreaks

a vector containing the bin boundaries of the cells along the X axis.

yBreaks

a vector containing the bin boundaries of the cells along the X axis.

xTotal

the total number of spikes of the "X" neuron.

yTotal

the total number of spikes of the "Y" neuron.

xFreq

the mean freqency of the "X" neuron.

yFreq

the mean freqency of the "Y" neuron.

nbTrials

the number of trials of xRT (and yRT).

acquisitionWindow

the boundaries of the acquisition window.

call

the matched call.

Note

I use "joint scatter diagram" for what Gerstein and Perkel (1972) more properly call a "joint peristimulus time scatter diagram".

Author(s)

Christophe Pouzat christophe.pouzat@gmail.com

References

Gerstein, G. L. and Perkel, D. H. (1972) Mutual temporal relationships among neuronal spike trains. Statistical techniques for display and analysis. Biophys J 12: 453–473. http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1484144

Aertsen, A. M., Gerstein, G. L., Habib, M. K., Palm, G. (1989) Dynamics of neuronal firing correlation: modulation of "effective connectivity". J Neurophysiol 61: 900–917. http://jn.physiology.org/cgi/content/abstract/61/5/900

See Also

lockedTrain, plot.lockedTrain, hist.lockedTrain, slockedTrain, plot.slockedTrain, contour, image, persp, attr, attributes

Examples

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## load e070528citronellal data
data(e070528citronellal)
## plot a jsd with neuron 1 on X and neuron 2 on Y
jsd(e070528citronellal[[1]],e070528citronellal[[2]])
## now make the jpsth
j1.2 <- jpsth(e070528citronellal[[1]],e070528citronellal[[2]])
## make a contour plot
contour(j1.2)
## make an image plot
image(j1.2)
## make a persp plot
persp(j1.2)
## get a data frame
j1.2DF <- jpsth2df(j1.2)
## fit a gam model assuming no interaction
## Not run: 
fitNoI <- gam(Count ~ s(X,k=100,bs="cr") + s(Y,k=100,bs="cr"),data=j1.2DF,family=poisson())

## End(Not run)


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