R/scalp.t.R

Defines functions scalp.t

Documented in scalp.t

scalp.t <-
function(base1, base2, numbers1, numbers2=NULL, paired=TRUE, alpha=0.05, sig=NULL, erplist1=NULL, erplist2=erplist1, smo=NULL, layout=1, ylims="auto", yrev=TRUE, startmsec=-200, endmsec=1200, lwd=c(1,1), lty=c(1,1), color.list=c("blue", "red"), legend=F, legend.lab="default", t.axis=seq(-100,endmsec,200), scalp.array=NULL) {


	# preliminary checks
	if (is.null(erplist1)|is.null(erplist2)){
	stop("two erplist objects (erplist1 and erplist2) containing ERP data frames must be specified!", call.=F)
	}
	
	# consistency checks for paired =T
	if (paired==TRUE&(length(numbers1)!=length(numbers2))){
	stop ("if paired == TRUE, numbers1 and numbers2 must have equal length.", call.=F)
	}
	
	#### object checks
	object.names1=paste(base1, numbers1, sep="")
	if (any(!object.names1%in%names(erplist1))){
		missing.objects1=object.names1[!object.names1%in%names(erplist1)]
		missing.object.collist1=paste(missing.objects1, "\n", sep="")
		stop("The following objects are not contained in the erplist1 specified:\n", missing.object.collist1, call.=F)
	}
		#### object checks
	object.names2=paste(base2, numbers2, sep="")
	if (any(!object.names2%in%names(erplist2))){
		missing.objects2=object.names2[!object.names2%in%names(erplist2)]
		missing.object.collist2=paste(missing.objects2, "\n", sep="")
		stop("The following objects are not contained in the erplist2 specified:\n", missing.object.collist2, call.=F)
	}
	




if (length(legend.lab)==1&legend.lab[1]=="default"){
	legend.lab=c(base1, base2)
}


#### PARTE 1: STATISTICHE PER ELETTRODO ####
if (is.null(numbers2)){
	numbers2=numbers1}


if (is.null(sig)){
	
element=function(x,row.i){
	return(x[row.i,])
	}

alldata1.list=list(NULL)
alldata2.list=list(NULL)
for (i1 in 1:length(numbers1)){
	alldata1.list[[i1]]=erplist1[[paste(base1,numbers1[i1], sep="")]]
	}
for (i2 in 1:length(numbers2)){
	alldata2.list[[i2]]=erplist2[[paste(base2,numbers2[i2], sep="")]]	
	}


alltemp=list(NULL)
length(alltemp)=dim(alldata1.list[[1]])[1] #creo una lista con tanti elementi quanti i punti del tracciato.
alltemp.results=list(NULL)
length(alltemp.results)=dim(alldata1.list[[1]])[1] #creo una lista con tanti elementi quanti i punti del tracciato.


## creo degli oggetti per stimare il tempo necessario ai calcoli
n.points.time=floor(seq(1,dim(alldata1.list[[1]])[1],dim(alldata1.list[[1]])[1]/10))
time.elapsed=0
##############


cat("t-test results computation\n")
for (k in 1:dim(alldata1.list[[1]])[1]) {#prendo la dimensione di un data.frame qualsiasi
		temp1=lapply(alldata1.list, function(x) { element(x,k) } )
		temp1.1=matrix(unlist(temp1), ncol=length(alldata1.list[[1]]), byrow=TRUE)
		temp2=lapply(alldata2.list, function(x) { element(x,k) } )
		temp2.1=matrix(unlist(temp2), ncol=length(alldata1.list[[1]]), byrow=TRUE) #di ciascuna riga una 
		#matrice con n righe (una per soggetto) e k colonne (una per elettrodo) 
		alltemp[[k]][[1]]=temp1.1
		alltemp[[k]][[2]]=temp2.1
		temp.results.vet=NULL
		for (j in 1:dim(alltemp[[k]][[1]])[2]){#nota:uso dim perché alltemp[[k]][[1]] è una matrice
		temp.results.vet[j]=(t.test(alltemp[[k]][[1]][,j], alltemp[[k]][[2]][,j], corr=F, paired=paired)$p.value)<alpha
		}
		alltemp.results[[k]]=temp.results.vet
		if (k%in%n.points.time){
			cat(rep(".",10-time.elapsed), "\n")
			time.elapsed=time.elapsed+1
			}
		}
		cat("\n")

alltemp.results=matrix(unlist(alltemp.results), byrow=TRUE, ncol=dim(alldata1.list[[1]])[2])
alltemp.results=as.data.frame(alltemp.results)
names(alltemp.results)=names(alldata1.list[[1]])
		}
if (!is.null(sig)){
	alltemp.results=sig
	}

##### PARTE 2 CREO DATAFRAME PER SCALP


### FUNZIONE PER FARE AVERAGE PER PLOT

#base1 = le prime lettere degli oggetti 
#numbers1= il numero dei soggetti di cui calcolare l'average

alldata1=grandaverage(base=base1, numbers1, erplist=erplist1)
alldata2=grandaverage(base=base2,numbers2, erplist=erplist2)

categ=list(alldata1,alldata2)

if (class(categ)!="list"){
		stop("input object must be a list!!")}
		

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 è 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")) {
			
			### NOTA: plotto due volte il grafico: la prima volta con type="n" poi con type="l". Altrimenti le bande si sovrascrivono col grafico
			el=categ[[1]][[electrodes[i]]][1:dim(categ[[1]])[1]]
			
			
			plot(el, type="n", 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])
			
			# plotto le bande di significatività
			######################
			abline(v=grep(TRUE,alltemp.results[,electrodes[i]]), col="lightgray")
			#######################
			
			if (!is.null(smo)){
				el=smooth.spline(el, spar=smo)
			}
			
			el=categ[[1]][[electrodes[i]]][1:dim(categ[[1]])[1]]

			### NOTA: plotto due volte il grafico: la prima volta con type="n" poi con type="l". Altrimenti le bande si sovrascrivono col grafico
			lines(el, col=color.list[1],  cex.main=0.85, lwd=lwd[1], lty=lty[1])

				##### di seguito ho semplicemente calcolato, tramite una proporzione, il punto che corrisponde allo 0
				zeropoint=msectopoints(0, length(el), startmsec, 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)
				
			el2=categ[[2]][[electrodes[i]]]
			if (!is.null(smo)){
				el2=smooth.spline(el2, spar=smo)
			}						
			lines(el2,col=color.list[2], lwd=lwd[2],lty=lty[2])

							
									 
		}
	}
par(oldpar)#questo pezzo è per resettare alla fine della funzione i vecchi parametri. L'ho preso da "An 
#introduction to R" pag. 68. Vedi anche sotto.
invisible(alltemp.results)
}

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erpR documentation built on May 31, 2017, 5:01 a.m.