In tdanker/ephys2: Read, analyze and plot HEKA Patchmaster files

The ephys2 package facilitates reading HEKA Patchmaster files into an R session, viewing the tree strucuture, extract and plot single traces or complete series, and perform analyses on them.

Examples

library(ephys2)
tree<-get_treeinfo(examplefile("NaV"))
s<-getSeries(tree,1,1,7)
s$set_cursor("peak", curMin_, c(0.0112,0.0117)) 
s$plot(xlim=c(.011, .013))

I/t plots

s$add_lpinfo(c(0,1,10, 100, 300, 1000), c(5,15,15,15,15,13), "Lidocaine")
RESULTS<-s$plotIt("peak", main="I/t plot", bty="l")
abline(h=0, lty=3, col="blue")

library(dplyr)
# change concentrations
#RESULTS$Concentration<-c(1,3,0,.1,.3)
# normalize
#RESULTS %>% arrange(Concentration)  -> RESULTS2
# drc
drc_(RESULTS, param=2)

I/V plots

The example file also contains a series that was recorded with the intention to make an I/V plot, showing the activation of the current over voltage. First, we set up the cursors and check the result:

s2<-getSeries(tree,1,1,3)
s2$set_cursor("peak", curMin_, c(0.0105,0.013))
s2$set_cursor("base", curMean_, c(0.0,0.002))
s2$plot()

Now, plotting the I/V relationship only requires setting up the stimulus voltages. Note how we use a plot formula to substract the base cursor:

make_stimulus(s2$sweeps, "voltage",base=-80,inc=10)
s2$plotresults(peak-base~voltage, type="o", main="activation of the NaV 1.4 sodium channel",  bty="l")