inst/extdata/render_ser.R

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

# This file is sourced each time a Series is selected in the tree.
# print("hi from render_ser")

# project setup script ####################################################################
# the idea is to provide initial settings for project first start 
# that may be modified interactively and not be overwritten by subsequent runs of the script

# typical setup script
setup_tree("VG_Blocker.dat", warn=F) # existing trees will not be overwritten. Maybe we can include a check for same filename!
init_cursor("NaIV", "min", curMin_, c(0.01,0.015))  # existing settings from previous sessions will not be overwritten
init_cursor("NaIV", "base", curMean_, c(0.005,0.009)) 
init_cursor("NaPharm", "base", curMean_, c(0.005,0.009)) 
init_cursor("NaPharm", "min", curMin_, c(0.01,0.015)) 
make_stimulus("NaIV", "voltage", -80, 10)

# the use of init_cursor above makes it save to define a resultmethods and plotting methods using the cursor
set_resultmethod("NaIV",name = "add_r1", function(x) {x$r1<-x$min*-1; x})
set_plotformula("NaIV", min-base~voltage)
set_plotformula("NaPharm", min~relTime)
set_plotformula("NaIV", min-base~voltage)

# bit of raw meat
  attr(tree[[1]],'PLXLSfiles')<- list("VG_Blocker_1.xls") #vorherst nur 1 möglich
set_plotformula("NaPharm", Online1~relTime)
#############################################################################################

.render_ser <- 
  function(...) {
    #plot(0, main="render_serx")
    str(selection_)
  }


# if this code is sourced automatically, use 
# <<- to store in global CURSORS, 
# <-  to store only in this session

# modified from get_selected_names:



####################################################
# functions to be included in package

get_checked<-function (tree, ancestry = NULL, vec = list()) 
{
  if (is.list(tree)) {
    for (i in 1:length(tree)) {
      anc <- c(ancestry, names(tree)[i])
      vec <- get_checked(tree[[i]], anc, vec)
    }
  }
  a <- attr(tree, "stchecked", TRUE)
  if (!is.null(a) && a == TRUE) {
    el <- tail(ancestry, n = 1)
    vec[length(vec) + 1] <- el
    attr(vec[[length(vec)]], "ancestry") <- head(ancestry, 
                                                 n = length(ancestry) - 1)
  }
  return(vec)
}

plot2.default <<-function(tree,inp.tree,...) {
  selection <- get_selected(inp.tree, format = "names")
  sel <- c(attr(selection[[1]], "ancestry"), selection[[1]]) 
  stimname<-attr(tree[[sel]], "StimulusName") #ephys2:::getStimname_from_node(tree[[sel]]) 
  r<-calculate.results(tree,selection)
  #print(r)
  x=as.character(CURSORS[[stimname]]$plotformula[3])
  y=as.character(CURSORS[[stimname]]$plotformula[2])
  if(!is.null(r)){
    require(ggplot2)
   
    p<-(ggplot(r, aes_string(x, y)) 
          +geom_line(aes(colour=factor(ser))) 
          +geom_point() 
    )
  }
  if(!is.null(r$Concentration)){
    if(!all(is.na(r$Concentration))){ #COncentration is set if a PLXLS is found and matched
      p<-p+ aes(colour=factor(Concentration)) 
    } 
  }
  
  print(p)
}

CURSORS$NaIV$plot2.fun           <<- plot2.default
CURSORS$NaPharm$plot2.fun        <<- plot2.default
CURSORS$'2PulseInact'$plot2.fun  <<-NULL