R/scalp.R

In erpR: Event-Related Potentials (ERP) Analysis, Graphics and Utility Functions

scalp <-
  function(erpdfs, smo=NULL, layout=1, ylims="auto", yrev=TRUE, startmsec=NULL, endmsec=NULL, lwd=1, lty=1, color.list=c("blue", "red", "darkgreen"), legend=F, legend.lab="default", t.axis=NULL, scalp.array=NULL){
    
    ### check esistenza
    ### check esistenza
    if (is.data.frame(erpdfs)){
      categ = list(erpdfs)
    } else {
      categ = erpdfs
    }
    
    if (class(categ)!="list"){
      stop("input object must be a list of erpdfs or an erpdf!")
    }
    
    ### get startmsec from the first object
    erpdf = categ[[1]]
    
    if(!is.null(attr(erpdf, "startmsec")) & !is.null(attr(erpdf, "endmsec"))){
      startmsec=attr(erpdf, "startmsec")
      endmsec=attr(erpdf, "endmsec")
    }
    
    if (is.null(startmsec)|is.null(endmsec)){
      stop("startmsec and endmsec must be specified", call.=F)
    }
    
    # create t.axis if not supplied (step by 200)
    if (is.null(t.axis)){
      t.axis=seq(startmsec, endmsec, 200)
    }
    
    
    if (length(legend.lab)==1&legend.lab[1]=="default"){
      legend.lab=deparse(substitute(erpdfs))
      legend.lab=gsub("\\(", "",legend.lab)
      legend.lab=gsub("\\)", "", legend.lab)
      legend.lab=gsub("^list", "", legend.lab)
      legend.lab=gsub(" ", "", legend.lab)
      legend.lab=unlist(strsplit(legend.lab, ","))
    }
    
    if (length(lwd)==1){
      lwd=rep(lwd, length(categ))}
    if (length(lty)==1){
      lty=rep(lty, length(categ))}
    
    ### ADD OUTER MARGIN
    par(oma=c(1,1,1,1))
    
    
    if (layout[1]==1){
      electrodes=c("yaxis","Fp1", "blank", "Fp2","legend", "F7", "F3", "FZ", "F4", "F8", "FT7", "FC3", "FCZ", "FC4", "FT8", "T3", "C3", "CZ","C4","T4","TP7", "CP3", "CPZ", "CP4", "TP8", "T5", "P3", "PZ", "P4", "T6", "xaxis", "O1", "OZ", "O2", "blank")
    }
    if (layout[1]==2){
      electrodes=c("yaxis","Fp1", "FPZ", "Fp2","legend", "F7", "F3", "FZ", "F4", "F8", "FT7", "FC3", "FCZ", "FC4", "FT8", "T7", "C3", "CZ","C4","T8","TP7", "CP3", "CPZ", "CP4", "TP8", "P7", "P3", "PZ", "P4", "P8", "xaxis", "O1", "OZ", "O2", "blank")
    }
    if (layout[1]==3){
      electrodes=c("yaxis","Fp1", "Fpz", "Fp2","legend", "F7", "F3", "FZ", "F4", "F8", "FT7", "FC3", "FCz", "FC4", "FT8", "T3", "C3", "Cz","C4","T4","TP7", "CP3", "CPz", "CP4", "TP8", "T5", "P3", "PZ", "P4", "T6", "xaxis", "O1", "blank", "O2", "blank")
    }
    if (layout[1]==4){
      electrodes=c("yaxis", "Fp1", "blank", "Fp2", "legend","blank", "AF3", "blank", "AF4", "blank", "F7", "F3", "Fz", "F4", "F8", "FC5", "FC1", "FCz", "FC2", "FC6", "T7", "C3", "Cz", "C4", "T8", "blank", "CP1", "CPz", "CP2", "blank", "P7", "P3", "Pz", "P4", "P8", "blank","O1","blank", "O2", "blank")
    }
    if (layout[1]==5){
      electrodes=c("yaxis", "Fp1", "Fpz", "Fp2", "legend","blank", "AF3", "blank", "AF4", "blank", "F7", "F3", "Fz", "F4", "F8", "FC5", "FC1", "blank", "FC2", "FC6", "T7", "C3", "Cz", "C4", "T8", "CP5", "CP1", "blank", "CP2", "CP6", "P7", "P3", "Pz", "P4", "P8","PO7", "PO3", "POz", "PO4", "PO8", "blank","O1","Oz", "O2", "blank" )
    }
    if (length(layout)>1){
      electrodes=layout
    }		
    
    ## ci sono incongruenze con le etichette degli elettrodi. Per non fermarmi le cambio momentaneamente nella seguente #maniera T7=T3, T4=T8, P7=T5, T6=P8
    
    if (ylims=="auto"){
      ## mergio tutti i dataset per riscalare gli assi rispetto a massimo e minimo 
      alldata=NULL
      for (i in 1:length(categ)){
        alldata=rbind(alldata, categ[[i]])
      }
      ymax=max(alldata)
      ymin=min(alldata)
      yedge=max(c(ymax, abs(ymin)))#calcolo questo yedge in modo da fare limiti delle y simmetrici
      # aggiungo una perecentuale per evitare che il grafico sbordi (il)
      yedge=c(-yedge,yedge)
    }
    if (ylims!="auto"){
      yedge=ylims
      yedge=c(-ylims, ylims)
    }	
    
    if (yrev==TRUE){
      yedge=sort(yedge, decreasing=T)
    }
    
    oldpar <- par(no.readonly=TRUE) #questo pezzo e per risettare alla fine della funzione i vecchi parametri. L'ho preso da "An introduction to R" pag. 68. Vedi anche sotto.
    par(mfrow=c(7,5), mai=c(0,0,0,0))
    if (layout[1]==5)
    {
      par(mfrow=c(10,5), mai=c(0,0,0,0))
    }
    if (layout[1]==4)
    {
      par(mfrow=c(8,5), mai=c(0,0,0,0))
    }
    if (!is.null(scalp.array)){
      par(mfrow=scalp.array, mai=c(0,0,0,0))
    }
    
    
    
    for (i in 1:(length(electrodes))){
      if (electrodes[i]=="yaxis"){
        plot(1, type="n", frame.plot=FALSE,xlim=c(1,dim(categ[[1]])[1]),xaxt="n",yaxt="n", ylim=c(yedge[1]+yedge[1]/3,yedge[2]+(yedge[2]/3)))
        axis(side=2, pos=dim(categ[[1]])[1]/2, at=c(round(ceiling(yedge[1]),0),round(ceiling(yedge[1])/2,0),0,round(floor(yedge[2])/2,0),round(floor(yedge[2]),0)), cex.axis=0.8, las=2)
        text((dim(categ[[1]])[1]/2)+(dim(categ[[1]])[1]/8),0, labels=expression(paste(mu,"V")), cex=1.4)
      }
      if (electrodes[i]=="blank") {
        plot.new()
      }
      if (electrodes[i]=="legend"){
        plot.new()
        if (legend=="TRUE"){
          legend("center", legend=legend.lab, col=color.list, cex=1.2, lty=lty, lwd=lwd) #pch=15, pt.bg=color.list
        }
      }
      if (electrodes[i]=="xaxis"){
        plot(1, type="n", frame.plot=FALSE,xlim=c(1,dim(categ[[1]])[1]),xaxt="n",yaxt="n", ylim=c(yedge[1]+yedge[1]/3,yedge[2]+(yedge[2]/3)))
        axis(1, pos=0, at=msectopoints(t.axis, dim(categ[[1]])[1], startmsec, endmsec), labels=paste(t.axis))
      }
      if (!electrodes[i]%in%c("xaxis", "yaxis", "legend", "blank")) {
        if(!is.null(smo)){
          el=smooth.spline(categ[[1]][[electrodes[i]]][1:dim(categ[[1]])[1]], spar=smo)
        } else {
          el=categ[[1]][[electrodes[i]]][1:dim(categ[[1]])[1]]
        }
        plot(el, type="l", ylim=c(yedge[1]+yedge[1]/3,yedge[2]+(yedge[2]/3)),col=color.list[1], main="", ylab="", xlab="", cex.main=0.85,xlim=c(1,dim(categ[[1]])[1]),xaxt="n",yaxt="n",frame.plot=FALSE, lwd=lwd[1], lty=lty[1])
        
        ##### di seguito ho semplicemente calcolato, tramite una proporzione, il punto che corrisponde allo 0
        
        totalendmsec=endmsec+abs(startmsec)
        zeropoint=msectopoints(0, dim(categ[[1]])[1], startmsec=startmsec, endmsec=endmsec)
        
        segments(x0=zeropoint, y0=-0.8, x1=zeropoint, y1=0.5, lwd=1.5)
        abline(h=0, lty="longdash")
        mtext(electrodes[i],side=3, line=-2)
        if (length(categ)>1&electrodes[i]!="blank") {
          for (k in 2:length(categ)){
            if(!is.null(smo)){
              el=smooth.spline(categ[[k]][[electrodes[i]]][1:dim(categ[[1]])[1]], spar=smo)
            } else {
              el=categ[[k]][[electrodes[i]]][1:dim(categ[[1]])[1]]
            }
            
            lines(el,col=color.list[k], lwd=lwd[k],lty=lty[k])
          }
        } 
      }
    }
    par(oldpar)#questo pezzo e per resettare alla fine della funzione i vecchi parametri. L'ho preso da "An 
    #introduction to R" pag. 68. Vedi anche sotto.
  }