PlotRasterFromSweeps: Make a raster plot from a set of Nclamp sweeps recording...

In jefferis/gphys: Analyse Electrophysiology Data Acquired by 'Neuromatic' / 'Igor Pro'

Description

This overloads base R's plot and calls PlotRasterFromSweeps

Usage

PlotRasterFromSweeps(sweepdir, sweeps, subdir = "", subset = NULL,
  xlim = NULL, xaxis = TRUE, yaxis = TRUE, frame.plot = TRUE,
  xaxs = "i", yaxs = "i", main, sub, xlab = "Time/ms",
  ylab = "Odour", pch = 22, dotcolour = "black", dotsize = 0.5,
  dotwidth = 20, spikeheight = 0.8, odourRange = NULL,
  odourCol = rgb(1, 0.8, 0.8, 1), relabelfun = identity,
  fixChannels = NULL, IncludeChannels = FALSE, PlotSpikes = TRUE,
  PlotDividers = TRUE, DividerCol = "black", DividerLwd = 0.5,
  panel.first = NULL, panel.last = NULL, ...)

## S3 method for class 'spiketimes'
plot(x, ...)

Arguments

sweepdir	directory containing Nclamp pxp sweep files
sweeps	Vector of sweeps to include (e.g. 1:7) or character regex which sweeps must match.
subdir	subdirectory containing group of spike times txt files
subset	Numeric vector of channels or character vector of odours
xlim	x axis range of plot
xaxis	(default TRUE)
yaxis	(default TRUE)
frame.plot	Plot a box around the whole plot (default TRUE)
xaxs, yaxs	Whether to extend xlim,ylim by 4 percent (see ?par, default FALSE)
main	main title of plot (see title)
sub	subtitle of plot
xlab	axis label (default Time/ms)
ylab	axis label (default odour)
pch	plotting character (default 22 is a square, see details for rect)
dotcolour	colour of dots in raster plot (default black)
dotsize	size of dots in raster plot (default 0.5)
dotwidth	Width in ms of rectangle when pch='rect'
spikeheight	Relative height of spike when pch='rect' (default 0.8)
odourRange	time window of odour delivery
odourCol	colour of odour window (default pale red)
relabelfun	function to apply to odour labels (default no relabelling)
fixChannels	Optional named integer vector that remaps some bad numeric channels to correct odours. FIXME shouldn't we fix channels as well.
IncludeChannels	include numeric id of odour channel (e.g. for blanks)
PlotSpikes	Whether to plot the spikes (default TRUE)
PlotDividers	Plot the dividing lines between odours (default TRUE)
DividerCol	the colour with which to plot dividing lines between odours (default black)
DividerLwd	the width of the lines between odours (default 0.5)
panel.first	An expression to be evaluated after the plot axes are set up but before any plotting takes place
panel.last	An expression to be evaluated after spikes have been plotted
...	Additional parameters passed to plot
x	A spiketimes object

Details

Note that can also give a spiketimes list from CollectSpikesFromSweeps By default the odour stimulus is represented by a pale red rectangle in a layer behind the spikes. If pch takes the special value "rect" then rectangles of width dotwidth are drawn. spikewidth will then specify the relative size of the spikes with 1 resulting in the top of spikes from one line at the same height as the base of spikes in the line above. If more than one stimulus is required, odourRange can be specified as a vector of successive start,stop times e.g. c(start1,stop1,start2,stop2).

Author(s)

jefferis

See Also

CollectSpikesFromSweeps, AddLinesToRasterPlot,fix.odd and plot.default for graphical parameters

PlotRasterFromSweeps, spiketimes

Examples

## Plot time range 2-4s with odour pulse 2-3s for sweeps 0,1,3
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20110811c0',package='gphys'),
  c(0,1,3),xlim=c(2000,4000),odourRange=c(2000,3000))
# Use rectangles for spikes instead
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20110811c0',package='gphys'),
  c(0,1,3),xlim=c(0,4000),odourRange=c(2000,3000),dotwidth=20,pch='rect')
## Fix a bad label, first define a function 
relabel=function(labels) {labels[labels=="fly"]="empty";labels}
## and then use it
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20110811c0',package='gphys'),
  c(0,1,3),relabelfun=relabel)
## Example with block based organisation 
## i.e. spike files sorted into different subdirs for each stimulus protocol
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20120514c2',package='gphys'),
  subdir='BLOCKA',odourRange=c(2000,2500),xlim=c(0,5000))
## Example of fixing one of Jonny's traces when channels were mixed up
fixVec=c(empty=31,IAA=30,cVA=29,PAA=27,`4ol`=26,ctr=25)
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20110907c3',package='gphys'),
  subdir='BLOCKI',odourRange=c(2000,2500),xlim=c(0,5000),fixChannels=fixVec)
## Imagine a double odour stimulation
PlotRasterFromSweeps(
  system.file('igor','spikes','nm20110907c3',package='gphys'),
  subdir='BLOCKI',odourRange=c(2000,2500,3000,3250),xlim=c(0,5000),
  fixChannels=fixVec)
options(gphys.datadir=system.file('igor','spikes',package='gphys'))
spikes=CollectSpikesFromSweeps('nm20120514c2',subdir='BLOCKB')
plot(spikes)

jefferis/gphys documentation built on June 5, 2019, 9:45 p.m.