jpsth {STAR} | R Documentation |
Some mainly graphical tools to probe interactions between 2 neurons recorded in the presence of a repeated stimulation.
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)
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 . |
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
.
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. |
I use "joint scatter diagram" for what Gerstein and Perkel (1972) more properly call a "joint peristimulus time scatter diagram".
Christophe Pouzat christophe.pouzat@gmail.com
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
lockedTrain
,
plot.lockedTrain
,
hist.lockedTrain
,
gsslockedTrain
,
plot.gsslockedTrain
,
gsslockedTrain0
,
plot.gsslockedTrain0
,
gamlockedTrain
,
plot.gamlockedTrain
,
contour
,
image
,
persp
,
attr
,
attributes
## 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)