jpsth {STAR}R Documentation

Related Functions and Methods for Joint-PSTHs and Joint Scatter Diagrams

Description

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

Usage

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 gssanova, gssanova0 or 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, gsslockedTrain, plot.gsslockedTrain, gsslockedTrain0, plot.gsslockedTrain0, gamlockedTrain, plot.gamlockedTrain, contour, image, persp, attr, attributes

Examples

## 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)
## Not run: 
## fit a gss model with interactions
## use a larger bin width for the jpsth
j1.2 <- jpsth(e070528citronellal[[1]],e070528citronellal[[2]],0.2,0.2)
## get a data frame
j1.2DF <- jpsth2df(j1.2)
## To save computation time start analyzing
## just before the stimulation time
j1.2DF <- j1.2DF[j1.2DF$X > 6 & j1.2DF$Y>6,]
gf <- gssanova(Count ~ X*Y, family="poisson", data=j1.2DF,seed=20061001)
## Use the project function of gss to check the significance
## of the interaction term
project(gf2,inc=c("X","Y"))
## End(Not run)
## Not run: 
## fit a gam model assuming no interaction
## get a data frame
j1.2DF <- jpsth2df(j1.2)
fitNoI <- gam(Count ~ s(X,k=100,bs="cr") + s(Y,k=100,bs="cr"),data=j1.2DF,family=poisson())
## End(Not run)

[Package STAR version 0.2-2 Index]