diff --git a/README.md b/README.md index 73d4194..219c339 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,7 @@ # gphys [![Build Status](https://travis-ci.org/jefferis/gphys.svg)](https://travis-ci.org/jefferis/gphys) [![Docs](https://img.shields.io/badge/docs-100%25-brightgreen.svg)](https://jefferis.github.io/gphys/reference/) -[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10300.svg)](https://doi.org/10.5281/zenodo.10300) +[![DOI](https://zenodo.org/badge/12226078.svg)](https://zenodo.org/badge/latestdoi/12226078) This R package provides relatively specialised routines for analysing electrophysiological data determined by the research in [our lab](http://jefferislab.org) using whole cell patch clamp techniques to analyse olfactory processing in the fly. Nevertheless it is possible that others, especially anyone using Jason Rothman's [Neuromatic](http://www.neuromatic.thinkrandom.com) data analysis and acquisition package for Igor Pro, may find some functionality useful. It can also be used to reproduce some of the analysis / figures in our published work e.g. in the package [frulhns](https://github.com/jefferis/frulhns). diff --git a/docs/index.html b/docs/index.html index 8d03f0e..d1b52e3 100644 --- a/docs/index.html +++ b/docs/index.html @@ -129,7 +129,7 @@

Dev status

diff --git a/docs/reference/OdourResponseFromSpikes.html b/docs/reference/OdourResponseFromSpikes.html index d0fb2fc..b942466 100644 --- a/docs/reference/OdourResponseFromSpikes.html +++ b/docs/reference/OdourResponseFromSpikes.html @@ -116,8 +116,8 @@

Produce table of spiking responses (optionally subtracting baseline)

- 
OdourResponseFromSpikes(spiketimes, responseWindow, baselineWindow = NULL,
-  freq = FALSE)
+ 
OdourResponseFromSpikes(spiketimes, responseWindow,
+  baselineWindow = NULL, freq = FALSE)

Arguments

diff --git a/docs/reference/PlotOdourResponseFromSpikes.html b/docs/reference/PlotOdourResponseFromSpikes.html index 18fc6f6..64c50d5 100644 --- a/docs/reference/PlotOdourResponseFromSpikes.html +++ b/docs/reference/PlotOdourResponseFromSpikes.html @@ -108,8 +108,8 @@

Boxplot of spikes within a window (optionally less a baseline)

- 
PlotOdourResponseFromSpikes(spiketimes, responseWindow, baselineWindow = NULL,
-  freq = FALSE, PLOTFUN = stripchart, ...)
+ 
PlotOdourResponseFromSpikes(spiketimes, responseWindow,
+  baselineWindow = NULL, freq = FALSE, PLOTFUN = stripchart, ...)

Arguments

diff --git a/docs/reference/PlotRasterFromSweeps.html b/docs/reference/PlotRasterFromSweeps.html index d7a1d8b..cd6a090 100644 --- a/docs/reference/PlotRasterFromSweeps.html +++ b/docs/reference/PlotRasterFromSweeps.html @@ -32,8 +32,7 @@ - + @@ -105,19 +104,19 @@

Make a raster plot from a set of Nclamp sweeps recording odour responses

-

Make a raster plot from a set of Nclamp sweeps recording odour responses

-

This overloads base R's plot and calls PlotRasterFromSweeps

+

This overloads base R's plot and calls PlotRasterFromSweeps

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, ...)
+  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 spiketimes
 plot(x, ...)
diff --git a/docs/reference/as.repeatedTrain.html b/docs/reference/as.repeatedTrain.html index 3fe35ac..cd5198a 100644 --- a/docs/reference/as.repeatedTrain.html +++ b/docs/reference/as.repeatedTrain.html @@ -32,8 +32,7 @@ - -

Generic function to convert spikes to STAR as.repeatedTrain objects

-

The STAR (Spike Train Analysis with R) package has a large number of useful +

The STAR (Spike Train Analysis with R) package has a large number of useful functions for e.g. PSTH analysis. Note that the spiketimes objects are a list of data frames, where each list element will correspond to one pxp file and will have trials for different diff --git a/docs/reference/gphys-package.html b/docs/reference/gphys-package.html index c6f182a..a63249a 100644 --- a/docs/reference/gphys-package.html +++ b/docs/reference/gphys-package.html @@ -133,7 +133,7 @@

Details appropriately at the start of a session or in your .Rprofile file. You can then use relative paths to your Igor data folders in the plot functions.

-

Finally as.repeatedTrain provides a bridge to the STAR +

Finally as.repeatedTrain provides a bridge to the STAR package which includes many spike analysis functions including (smoothed) peristimulus time histograms.

diff --git a/docs/reference/plot.mpsth.html b/docs/reference/plot.mpsth.html index 2c307ef..1d4c282 100644 --- a/docs/reference/plot.mpsth.html +++ b/docs/reference/plot.mpsth.html @@ -110,9 +110,9 @@

Plot PSTHs for multiple neurons (or multiple stimuli)

# S3 method for mpsth
 plot(x, stimTimeCourse = NULL, colStim = "grey80",
-  colCI = NULL, xlab = "Time /s", ylab = "Spike Freq /Hz", xlim, ylim,
-  lwd = 2, col = 1, labels = NULL, toplot = c("lines", "CI", "legend"),
-  ...)
+ colCI=NULL, xlab="Time /s", ylab="Spike Freq /Hz", xlim, + ylim, lwd=2, col=1, labels=NULL, toplot=c("lines", "CI", + "legend"), ...)

Arguments

diff --git a/docs/reference/read.odd.html b/docs/reference/read.odd.html index 82c3d57..117ff81 100644 --- a/docs/reference/read.odd.html +++ b/docs/reference/read.odd.html @@ -108,7 +108,8 @@

Read in the ODD text file describing odour presentation sequence

- 
read.odd(oddfile, fill = TRUE, stringsAsFactors = FALSE, Verbose = FALSE)
+ 
read.odd(oddfile, fill = TRUE, stringsAsFactors = FALSE,
+  Verbose = FALSE)

Arguments

diff --git a/docs/reference/set_finder_colour.html b/docs/reference/set_finder_colour.html index 24872c7..204e702 100644 --- a/docs/reference/set_finder_colour.html +++ b/docs/reference/set_finder_colour.html @@ -113,8 +113,8 @@

Set the colour label of a file in the MacOS X Finder - 
set_finder_colour(filename, col = c("None", "Gray", "Grey", "Green", "Purple",
-  "Blue", "Yellow", "Red", "Orange"))
+ 
set_finder_colour(filename, col = c("None", "Gray", "Grey", "Green",
+  "Purple", "Blue", "Yellow", "Red", "Orange"))

Arguments