R/XPSSurveyUtilities.r
In GSperanza/RxpsG_2.3-1: Processing Tool for X-ray Photoelectron Spectroscopy Data
Defines functions
DispLab
plotPeaks
ShowTablePeaks
AllElements
CoreLinesMaxRSF
NearerElement
FindElmtList
peakIdentificationOld
peakIdentification
peakDetection
ReadElmtList
## ===============================
## Identification of survey peaks
## ===============================
#--- function to read the Coreline table and identify elements
#--- A CoreLineTable is read containing a list of elements OK for Scienta and Kratos spectra
ReadElmtList<-function(SpectrumType){
switch(SpectrumType,
"CoreLines" = { fp <- system.file("extdata/CoreLinesTable.lib", package="RxpsG") },
"AugerTransitions" = { fp <- system.file("extdata/AugerTransitionsTable.lib", package="RxpsG")}
)
if (file.exists(fp)) {
ElmtList <- scan(fp, skip=0, sep="", what = list("character", "character", "numeric", "numeric", "numeric", "numeric"), quiet=TRUE)
ElmtList[[3]] <- as.numeric(ElmtList[[3]])
ElmtList[[4]] <- as.numeric(ElmtList[[4]])
ElmtList[[5]] <- as.numeric(ElmtList[[5]])
ElmtList[[6]] <- as.numeric(ElmtList[[6]])
ElmtList <- as.data.frame(ElmtList, stringsAsFactors = FALSE) # set it to FALSE
names(ElmtList) <- c("Element", "Orbital", "BE", "KE", "RSF_K", "RSF_S")
cat("\n ==>", SpectrumType, " Table loaded \n")
if (SpectrumType == "AugerTransitions") { names(ElmtList)[2] <- "Transition" }
return(ElmtList)
} else {
gmessage(msg=paste("ATTENTION:", SpectrumType, "file not Found. Check RxpsG package",sep=" "), title = "WARNING",icon = "warning" )
return()
}
}
peakDetection <- function(object, snmin , Ewin) {
#- find peaks: DO NOT use baseline(object, method = "peakDetection")
#- because it does not return the peaks index
import::from(baselin, baseline.peakDetection)
peaks <- baseline.peakDetection(matrix(data=object[[2]], nrow=1),
snminimum = snmin,
left.right = Ewin,
lwin.rwin = Ewin)
#- subset peaks
peaks <- peaks[c("baseline","corrected", "peaks")]
idx <- unlist(peaks$peaks) ## peaks index
#- coordinate dei picchi
positionsCorr <- list(x=object$x[idx], y=peaks$corrected[1,idx])
positionsOrig <- list(x=object$x[idx], y=object[[2]][idx])
#- sort positions per intensity
#- idx <- order(positionsCorr$y, decreasing=TRUE)
#- peaks ordered from High BE to low BE
idx <- c(1:length(positionsCorr$x))
peaks$table <- list(BE=positionsCorr$x[idx],
corr=positionsCorr$y[idx],
orig=positionsOrig$y[idx])
names(peaks$table$BE) <- rep(NA, length(peaks$table$BE))
return(invisible(peaks))
}
#---Identify peaks in the survey spectrum
peakIdentification <- function(peaks, DeltaEnergy, object, SpectrumType, ElmtList) {
RecPlot<-recordPlot() #save graph for UNDO option
#-- init
ElmtList1 <- ReadElmtList("CoreLines") #reads the CoreLine/Auger List Table
ElmtList1 <- format(ElmtList1, justify="centre", width=10)
ElmtList1 <- as.data.frame(ElmtList1, stringsAsFactors = FALSE)
ElmtList2 <- ReadElmtList("AugerTransitions") #reads the CoreLine/Auger List Table
ElmtList2 <- format(ElmtList2, justify="centre", width=10)
ElmtList2 <- as.data.frame(ElmtList2, stringsAsFactors = FALSE)
ElemLbl1 <- gsub(" ", "", ElmtList1[,1], fixed=TRUE) #suppress white spaces
ElemLbl2 <- gsub(" ", "", ElmtList2[,1], fixed=TRUE) #suppress white spaces
peaks$table$BE <- unname(peaks$table$BE) # length of the list of identified peaks
ElmntTbl1 <- data.frame()
ElmntTbl2 <- data.frame()
FoundElmnt <- NULL
NElmnt <- 0
NOrbit <- NULL
BE<-FALSE #set KE scale
if (object@Flags[1]) { # if object@Flags[1] == TRUE spectra are on a BE scale
BE <- TRUE
Eidx=3 #BE column in the ElemenList tables
} else {
Eidx=4 #KE column in the ElemenList tables
}
peakIdx <- 1
#-- loop on peaks
for (peakIdx in seq_along(peaks$table$BE)){
#-- if the peak is not assigned find for the element having higher RSF to that BE value
NewElmnt<-NULL
energy <- peaks$table$BE[peakIdx]
NewElmnt <- FindElmtList(energy, DeltaEnergy, BE, ElmtList1) #list of elements matching the energy value
if (length(NewElmnt)==0) {
txt <- paste("No elements found at energy: ", energy)
gmessage(msg=txt, title="NO ELEMENTS FOUND", icon="warning")
} else {
for (ii in seq_along(NewElmnt$Element)){ # Control if non void elements are present in the FoundElements list
Elmnt <- NewElmnt$Element[ii]
Elmnt <- gsub(" ", "", Elmnt, fixed=TRUE) #suppress white spaces
idx <- grep(Elmnt, FoundElmnt) #check if the found element was already identified or discarded
if (length(idx)==0) { #the element found is new and not already present in list of FoundElements
if (length(Elmnt)==0){ #finds peak falling at energy position in the survey
idx<-findXIndx(object[[1]], energy) #find index corresponding to x=energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??" #display ?? for non identified spectral feature
DispLab(list(x=energy,y=intensity), label=newlab)
EE<-as.character(peaks$table$BE[peakIdx])
cat("\n Warning: No Element found at energy ", EE, "Skip value")
peakIdx <- peakIdx+1 #skip the peak
}
cat("\n Found Element: ", Elmnt)
replayPlot(RecPlot) #restore original plot
idx1 <- which(Elmnt == ElemLbl1) #greep does not work: if Elmnt=="O" extracts rows corresponding to "O" and "Os"
Yrng<-range(object[[2]])
for (jj in seq_along(ElmtList1[idx1,Eidx])){
xx <- ElmtList1[idx1[jj],Eidx]
lines(x=c(xx, xx), y=Yrng, col="red") #plot CORELINES of the selected elements
}
idx2 <- which(Elmnt == ElemLbl2) #greep does not work: if Elmnt=="O" extracts rows corresponding to "O" and "Os"
for (jj in seq_along(ElmtList2[idx2,Eidx])){
xx <- ElmtList2[idx2[jj],Eidx]
lines(x=c(xx, xx), y=Yrng, col="blue") #plot AUGER TRANSITIONS of the selected elements
}
txt <- paste("Found correlation with ", Elmnt, " Core Lines. \nCorrect identification?", sep="")
answ=gconfirm(txt, title="FOUND ELEMENT", icon="warning")
if (answ) {
ElmntTbl1 <- rbind(ElmntTbl1, ElmtList1[idx1, ])
NElmnt <- NElmnt + 1
NOrbit[NElmnt] <-length(ElmtList1[idx1,2]) #number of orbitals of the identified element
ElmntTbl2 <- rbind(ElmntTbl2, ElmtList2[idx2, ])
}
FoundElmnt <- paste(FoundElmnt, Elmnt, sep=" ")
}
}
}
} #end external for on detected peak
replayPlot(RecPlot) #restore original plot
#now plot all the identified corelines and auger transition to show how many peaks are assigned
for (jj in seq_along(ElmntTbl1$Element)){
xx <- ElmntTbl1[jj,Eidx]
lines(x=c(xx, xx), y=Yrng, col="red") #plot CORELINES of the selected elements
}
for (jj in seq_along(ElmntTbl2$Element)){
xx <- ElmntTbl2[jj,Eidx]
lines(x=c(xx, xx), y=Yrng, col="blue") #plot CORELINES of the selected elements
}
gmessage(msg=" Please look at identified peaks if they describes all the spectral features.\n Otherwise Refresh plot, change identification precision and repeat the analysis.", title="IDENTIFICATION RESULTS", icon="warning")
if (length(ElmntTbl1$Element) == 0 ){
return()
} else {
replayPlot(RecPlot) #restore original plot
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/25 #vertical shift to not superpose labels
posLbl <- NULL
arrow <- TRUE
kk <- 1
for(ii in 1:NElmnt){
for(jj in 1:NOrbit[ii]){ #this for runs on the element orbitals which may be at same energy
energy <- as.numeric(ElmntTbl1$BE[kk]) #kk runs on the ElmntTable rows
idx <- findXIndex(object[[1]], energy)
intensity <- object[[2]][idx]
posLbl<-intensity+DeltaY*jj #jj increments for differen orbital same element
if (SpectrumType =="CoreLines"){
newlab <- paste(ElmntTbl1$Element[kk], ElmntTbl1$Orbital[kk], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl), label=newlab, arrow, direction="right", color="blue")
} else if (SpectrumType == "AugerTransitions") {
newlab <- paste(ElmntTbl1[ii,"Element"], ElmntTbl1[ii,"Transition"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
kk <- kk+1 #kk runs on the ElmntTbl1 rows: it is not simply ii+jj because every new ii jj restarts from 1
}
}
}
return(ElmntTbl1)
}
#---Identify peaks in the survey spectrum
peakIdentificationOld <- function(peaks, DeltaEnergy, object, SpectrumType, ElmtList) {
## init
PeaksLen <- length(peaks$table$BE) # length identified peaks
## loop on peaks starting from that having highest intensity
EleTable <- data.frame()
BE<-FALSE #set KE scale
if (object@Flags[1]) { BE=TRUE } # if BE TRUE if spectra are on a BE scale
for (peakIndex in 1:PeaksLen) {
posLbl <- NULL
elmLbl <- NULL
# DEn = 0.25
## if the peak is not assigned find for the element having higher RSF to that BE value
NewElement<-NULL
energy <- peaks$table$BE[peakIndex]
NewElements <- FindElmtList(energy, DeltaEnergy, BE, ElmtList)
if (is.null(NewElements)){
idx<-max(which(object[[1]] > energy)) #find all elements > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
EE<-as.character(peaks$table$BE[peakIndex])
cat("\n Warning: No Element found at energy ", EE, " Please check Energy scale Alignment!")
}
EleTable<-rbind(EleTable, NewElements) #for a given energy a list of element falling in the range: energy-DEn, energy+DEn is produced
elmLbl<-rbind(elmLbl, NewElements) #here only the elements found nearby the energy value
if (is.null(elmLbl)) {
# do nothing!
} else {
idx<-max(which(object[[1]]> energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
##print LBL elementi trovati
Nrw<-nrow(elmLbl)
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Y boundaries
intensity <- Yrng[2] - Nrw*DeltaY #shift to lower y
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for(ii in 1:Nrw){
if (length(elmLbl)>0 && SpectrumType =="CoreLines"){
newlab <- paste(elmLbl[ii,"Element"], elmLbl[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(elmLbl)>0 && SpectrumType == "AugerTransitions") {
newlab <- paste(elmLbl[ii,"Element"], elmLbl[ii,"Transition"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow=FALSE
}
}
}
names(EleTable)<-c("Element", "Orbital", "BE", "KE", "RSF_K", "RSF_S")
return(EleTable)
}
#---Function to extract list of elements in a given energy interval
FindElmtList<-function(energy, DeltaEnergy, BE, ElmtList){
EleTable<-NULL
if (BE) {
Escale="BE"
} else {
Escale="KE"
}
ElmtList[,Escale] <- as.numeric(ElmtList[,Escale])
EleTable <- subset(ElmtList, ElmtList[,Escale] >= energy-DeltaEnergy) #extract all element with energy >= energy+DeltaEnergy
EleTable <- subset(EleTable, EleTable[,Escale] <= energy+DeltaEnergy) #from that list select those with energy <= energy+DeltaEnergy
if (nrow(EleTable) == 0){ EleTable<-NULL }
return(EleTable)
}
#--- find first element in list whose position is close to 'energy' less than DeltaEnergy
NearerElement <- function(energy, DeltaEnergy, object, ElmtList) {
energy<-as.numeric(energy)
BE<-FALSE #imposto KE
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-NULL
DEn = 0.3
while(is.null(EleTable)){
EleTable<-FindElmtList(energy, DEn, BE, ElmtList)
DEn <- DEn + 0.2
if (DEn > DeltaEnergy) {
cat("\n No elements found with the selected precision!")
break
}
}
idx<-max(which(object[[1]]> energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[1,"Element"], EleTable[1,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[1,"Element"], EleTable[1,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else {
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
}
if (!is.null(EleTable)) {
space<-data.frame(Element=" ", Orbital=" ", BE=" ", KE=" ", RSF_K=" ", RSF_S=" ")
EleTable<-rbind(EleTable, space)
}
return(EleTable)
}
#--- Check All elements which RSFmax distance is less than DeltaEnergy
CoreLinesMaxRSF <- function(energy, DeltaEnergy=3, object, ElmtList) { #, index=1
posLbl <- NULL
energy<-as.numeric(energy)
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-FindElmtList(energy, DeltaEnergy, BE, ElmtList)
if (object@Flags[3] == TRUE){
idx<-which(EleTable[ ,6] == max(EleTable[ ,6]), arr.ind = TRUE) #search for the max in the RSF column Scienta
} else {
idx<-which(EleTable[ ,5] == max(EleTable[ ,5]), arr.ind = TRUE) #search for the max in the RSF column Kratos
}
EleTable<-EleTable[idx,] #select the EleTable-row with max RSF
Nrw<-nrow(EleTable)
if (is.null(Nrw)) {
#--- object[[1]] $x values, object[[2]] $y values
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
} else if (Nrw > 0) {
ii=1
#--- If same element repeats itself in the EleTable only that wit max RSF is kept
while(ii < Nrw){ #cannot use a FOR-loop since it is not sensitive to Nrw changes
element<-EleTable[ii,1] #
RepIndx<-grep(element, EleTable[ ,1]) #how many times an element is present in the EleTable
MaxIndx<-which(EleTable[RepIndx,3]==max(EleTable[RepIndx,3]), arr.ind=TRUE) #select the max RSF among EleTable-rows
LL<-length(RepIndx) #N. rows of tmp
for (jj in LL:1){ #ATTENZIONE: regressive FOR because rows are cancelled from the EleTable
if (RepIndx[jj] != RepIndx[MaxIndx]){ #if the EleTable-row hasn't max RSF
EleTable<-EleTable[-RepIndx[jj], ] #drop the EleTable-row
Nrw<-Nrw-1
}
}
ii<-ii+1
}
Nrw<-nrow(EleTable)
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-object[[2]][idx]
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Ygraph boundaries
intensity <- Yrng[2] - Nrw*DeltaY
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for (ii in 1:Nrw){
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow=FALSE
}
}
return(EleTable)
}
#--- Find ANY element with energy
AllElements <- function(energy, DeltaEnergy=2, object, ElmtList) {
posLbl <- NULL
posY <- NULL
energy<-as.numeric(energy)
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-FindElmtList(energy, DeltaEnergy, BE, ElmtList)
Nrw<-nrow(EleTable)
if (is.null(Nrw)) {
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else if (Nrw > 0) {
idx<-max(which(object[[1]] > energy))
intensity<-max(object[[2]][(idx-5):(idx+5)])
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Ygraph boundaries
intensity <- Yrng[2] - Nrw*DeltaY
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for (ii in 1:Nrw){
idx<-max(which(object[[1]] > energy))
intensity<-object[[2]][idx]
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow<-FALSE
}
}
return(EleTable)
}
#--- prints the ElementTable in a formatted fashion
ShowTablePeaks <- function(EleTable, SpectrumType) {
if(SpectrumType == "CoreLines") { Wdth=10 }
if(SpectrumType == "AugerTransitions") { Wdth=12 }
cat("\n\n\n ***** IDENTIFIED ELEMENTS ***** \n")
LL<-nrow(EleTable)
sss<-format(names(EleTable), justify="right", width=Wdth)
cat("\n", sss)
for(ii in 1:LL){
sss<-as.character(gsub(" ", "", EleTable[ii, ], fixed=TRUE))
sss<-format(sss, justify="right", width=Wdth)
cat("\n",sss)
}
}
plotPeaks <- function(object, peaks=NULL, type = c("normal","corrected"), ...) {
if (is.null(peaks) ) stop("\npeaks is NULL")
type <- match.arg(type)
## plot curve
if (type == "normal") {
plot(object)
lines(object$x, peaks$baseline[1,], col=2) ## baseline
points(peaks$table$BE, peaks$table$orig, col=3, cex=1.0) ## peaks
} else {
plot(object$x, peaks$corrected[1,], type="l", xlim=rev(c(range(object$x))), xlab=object@units[1], ylab=object@units[2], main = object@Symbol )
points(peaks$table$BE, peaks$table$corr, col=3, cex=1.0) ## peaks
}
## Peaks Label
if ( ! all(is.na(names(peaks$table$BE)) ) ) {
for (PeakBEIndx in seq_along(peaks$table$BE)) {
if (type == "normal") {
DispLab(list(x=peaks$table$BE[PeakBEIndx],
y=peaks$table$orig[PeakBEIndx]),
label=names(peaks$table$BE[PeakBEIndx]),
arrow=TRUE,
direction="right",
...)
} else {
DispLab(list(x=peaks$table$BE[PeakBEIndx],
y=peaks$table$corr[PeakBEIndx]),
label=names(peaks$table$BE[PeakBEIndx]),
arrow=TRUE,
direction="right",
...)
}
}
}
}
DispLab <- function(position.list,
label,
color="blue",
arrow = TRUE,
xspanf = 1, yspanf = 3, lenarrow = 0.08,
direction = c("right", "left", "center"),
...) {
# position.list = list(x,y)
direction <- match.arg(direction)
X0 <- position.list$x
# orizontal segment xspanf % of xrange
xspan <- abs(par("usr")[2]-par("usr")[1]) * xspanf/100
# vertical segment 3% of yrange
yspan <- abs(par("usr")[4]-par("usr")[3]) * yspanf/100
Yspan <- rep(yspan, length(X0))
# reverse yspan if y+2*yspan > ymax
if (any((position.list$y + 2*yspan) > par("usr")[4])) {
Yspan[which((position.list$y + 2*yspan) > par("usr")[4])] <- -yspan
}
Y0 <- position.list$y + 2*Yspan
Y1 <- position.list$y + Yspan
Y2 <- position.list$y + 3*Yspan
# arrow from(x0,y0) to (x1,y1)
if (arrow) {
arrows(X0, Y0, X0, Y1, length = lenarrow, col = color)
switch(direction,
"right" = {
X1 <- X0 + xspan
#segments(X0,Y0, X1, Y0, col=color)
text(X1, Y0, labels = label, col=color, pos=4, offset=0.5, ...)## etichetta
},
"left" = {
X1 <- X0 - xspan
#segments(X0,Y0, X1, Y0, col=color)
text(X1, Y0, labels = label, col=color, pos=2, offset=0.5, ...)## etichetta
},
"center" = {
text(X0, Y0, labels = label, col=color, pos=3, offset=0.5, ...)## etichetta
}
)
}
else text(X0, Y0, labels = label, pos=4, col=color, ...)
}
GSperanza/RxpsG_2.3-1 documentation built on Feb. 11, 2024, 5:09 p.m.
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Defines functions DispLab plotPeaks ShowTablePeaks AllElements CoreLinesMaxRSF NearerElement FindElmtList peakIdentificationOld peakIdentification peakDetection ReadElmtList
## ===============================
## Identification of survey peaks
## ===============================
#--- function to read the Coreline table and identify elements
#--- A CoreLineTable is read containing a list of elements OK for Scienta and Kratos spectra
ReadElmtList<-function(SpectrumType){
switch(SpectrumType,
"CoreLines" = { fp <- system.file("extdata/CoreLinesTable.lib", package="RxpsG") },
"AugerTransitions" = { fp <- system.file("extdata/AugerTransitionsTable.lib", package="RxpsG")}
)
if (file.exists(fp)) {
ElmtList <- scan(fp, skip=0, sep="", what = list("character", "character", "numeric", "numeric", "numeric", "numeric"), quiet=TRUE)
ElmtList[[3]] <- as.numeric(ElmtList[[3]])
ElmtList[[4]] <- as.numeric(ElmtList[[4]])
ElmtList[[5]] <- as.numeric(ElmtList[[5]])
ElmtList[[6]] <- as.numeric(ElmtList[[6]])
ElmtList <- as.data.frame(ElmtList, stringsAsFactors = FALSE) # set it to FALSE
names(ElmtList) <- c("Element", "Orbital", "BE", "KE", "RSF_K", "RSF_S")
cat("\n ==>", SpectrumType, " Table loaded \n")
if (SpectrumType == "AugerTransitions") { names(ElmtList)[2] <- "Transition" }
return(ElmtList)
} else {
gmessage(msg=paste("ATTENTION:", SpectrumType, "file not Found. Check RxpsG package",sep=" "), title = "WARNING",icon = "warning" )
return()
}
}
peakDetection <- function(object, snmin , Ewin) {
#- find peaks: DO NOT use baseline(object, method = "peakDetection")
#- because it does not return the peaks index
import::from(baselin, baseline.peakDetection)
peaks <- baseline.peakDetection(matrix(data=object[[2]], nrow=1),
snminimum = snmin,
left.right = Ewin,
lwin.rwin = Ewin)
#- subset peaks
peaks <- peaks[c("baseline","corrected", "peaks")]
idx <- unlist(peaks$peaks) ## peaks index
#- coordinate dei picchi
positionsCorr <- list(x=object$x[idx], y=peaks$corrected[1,idx])
positionsOrig <- list(x=object$x[idx], y=object[[2]][idx])
#- sort positions per intensity
#- idx <- order(positionsCorr$y, decreasing=TRUE)
#- peaks ordered from High BE to low BE
idx <- c(1:length(positionsCorr$x))
peaks$table <- list(BE=positionsCorr$x[idx],
corr=positionsCorr$y[idx],
orig=positionsOrig$y[idx])
names(peaks$table$BE) <- rep(NA, length(peaks$table$BE))
return(invisible(peaks))
}
#---Identify peaks in the survey spectrum
peakIdentification <- function(peaks, DeltaEnergy, object, SpectrumType, ElmtList) {
RecPlot<-recordPlot() #save graph for UNDO option
#-- init
ElmtList1 <- ReadElmtList("CoreLines") #reads the CoreLine/Auger List Table
ElmtList1 <- format(ElmtList1, justify="centre", width=10)
ElmtList1 <- as.data.frame(ElmtList1, stringsAsFactors = FALSE)
ElmtList2 <- ReadElmtList("AugerTransitions") #reads the CoreLine/Auger List Table
ElmtList2 <- format(ElmtList2, justify="centre", width=10)
ElmtList2 <- as.data.frame(ElmtList2, stringsAsFactors = FALSE)
ElemLbl1 <- gsub(" ", "", ElmtList1[,1], fixed=TRUE) #suppress white spaces
ElemLbl2 <- gsub(" ", "", ElmtList2[,1], fixed=TRUE) #suppress white spaces
peaks$table$BE <- unname(peaks$table$BE) # length of the list of identified peaks
ElmntTbl1 <- data.frame()
ElmntTbl2 <- data.frame()
FoundElmnt <- NULL
NElmnt <- 0
NOrbit <- NULL
BE<-FALSE #set KE scale
if (object@Flags[1]) { # if object@Flags[1] == TRUE spectra are on a BE scale
BE <- TRUE
Eidx=3 #BE column in the ElemenList tables
} else {
Eidx=4 #KE column in the ElemenList tables
}
peakIdx <- 1
#-- loop on peaks
for (peakIdx in seq_along(peaks$table$BE)){
#-- if the peak is not assigned find for the element having higher RSF to that BE value
NewElmnt<-NULL
energy <- peaks$table$BE[peakIdx]
NewElmnt <- FindElmtList(energy, DeltaEnergy, BE, ElmtList1) #list of elements matching the energy value
if (length(NewElmnt)==0) {
txt <- paste("No elements found at energy: ", energy)
gmessage(msg=txt, title="NO ELEMENTS FOUND", icon="warning")
} else {
for (ii in seq_along(NewElmnt$Element)){ # Control if non void elements are present in the FoundElements list
Elmnt <- NewElmnt$Element[ii]
Elmnt <- gsub(" ", "", Elmnt, fixed=TRUE) #suppress white spaces
idx <- grep(Elmnt, FoundElmnt) #check if the found element was already identified or discarded
if (length(idx)==0) { #the element found is new and not already present in list of FoundElements
if (length(Elmnt)==0){ #finds peak falling at energy position in the survey
idx<-findXIndx(object[[1]], energy) #find index corresponding to x=energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??" #display ?? for non identified spectral feature
DispLab(list(x=energy,y=intensity), label=newlab)
EE<-as.character(peaks$table$BE[peakIdx])
cat("\n Warning: No Element found at energy ", EE, "Skip value")
peakIdx <- peakIdx+1 #skip the peak
}
cat("\n Found Element: ", Elmnt)
replayPlot(RecPlot) #restore original plot
idx1 <- which(Elmnt == ElemLbl1) #greep does not work: if Elmnt=="O" extracts rows corresponding to "O" and "Os"
Yrng<-range(object[[2]])
for (jj in seq_along(ElmtList1[idx1,Eidx])){
xx <- ElmtList1[idx1[jj],Eidx]
lines(x=c(xx, xx), y=Yrng, col="red") #plot CORELINES of the selected elements
}
idx2 <- which(Elmnt == ElemLbl2) #greep does not work: if Elmnt=="O" extracts rows corresponding to "O" and "Os"
for (jj in seq_along(ElmtList2[idx2,Eidx])){
xx <- ElmtList2[idx2[jj],Eidx]
lines(x=c(xx, xx), y=Yrng, col="blue") #plot AUGER TRANSITIONS of the selected elements
}
txt <- paste("Found correlation with ", Elmnt, " Core Lines. \nCorrect identification?", sep="")
answ=gconfirm(txt, title="FOUND ELEMENT", icon="warning")
if (answ) {
ElmntTbl1 <- rbind(ElmntTbl1, ElmtList1[idx1, ])
NElmnt <- NElmnt + 1
NOrbit[NElmnt] <-length(ElmtList1[idx1,2]) #number of orbitals of the identified element
ElmntTbl2 <- rbind(ElmntTbl2, ElmtList2[idx2, ])
}
FoundElmnt <- paste(FoundElmnt, Elmnt, sep=" ")
}
}
}
} #end external for on detected peak
replayPlot(RecPlot) #restore original plot
#now plot all the identified corelines and auger transition to show how many peaks are assigned
for (jj in seq_along(ElmntTbl1$Element)){
xx <- ElmntTbl1[jj,Eidx]
lines(x=c(xx, xx), y=Yrng, col="red") #plot CORELINES of the selected elements
}
for (jj in seq_along(ElmntTbl2$Element)){
xx <- ElmntTbl2[jj,Eidx]
lines(x=c(xx, xx), y=Yrng, col="blue") #plot CORELINES of the selected elements
}
gmessage(msg=" Please look at identified peaks if they describes all the spectral features.\n Otherwise Refresh plot, change identification precision and repeat the analysis.", title="IDENTIFICATION RESULTS", icon="warning")
if (length(ElmntTbl1$Element) == 0 ){
return()
} else {
replayPlot(RecPlot) #restore original plot
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/25 #vertical shift to not superpose labels
posLbl <- NULL
arrow <- TRUE
kk <- 1
for(ii in 1:NElmnt){
for(jj in 1:NOrbit[ii]){ #this for runs on the element orbitals which may be at same energy
energy <- as.numeric(ElmntTbl1$BE[kk]) #kk runs on the ElmntTable rows
idx <- findXIndex(object[[1]], energy)
intensity <- object[[2]][idx]
posLbl<-intensity+DeltaY*jj #jj increments for differen orbital same element
if (SpectrumType =="CoreLines"){
newlab <- paste(ElmntTbl1$Element[kk], ElmntTbl1$Orbital[kk], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl), label=newlab, arrow, direction="right", color="blue")
} else if (SpectrumType == "AugerTransitions") {
newlab <- paste(ElmntTbl1[ii,"Element"], ElmntTbl1[ii,"Transition"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
kk <- kk+1 #kk runs on the ElmntTbl1 rows: it is not simply ii+jj because every new ii jj restarts from 1
}
}
}
return(ElmntTbl1)
}
#---Identify peaks in the survey spectrum
peakIdentificationOld <- function(peaks, DeltaEnergy, object, SpectrumType, ElmtList) {
## init
PeaksLen <- length(peaks$table$BE) # length identified peaks
## loop on peaks starting from that having highest intensity
EleTable <- data.frame()
BE<-FALSE #set KE scale
if (object@Flags[1]) { BE=TRUE } # if BE TRUE if spectra are on a BE scale
for (peakIndex in 1:PeaksLen) {
posLbl <- NULL
elmLbl <- NULL
# DEn = 0.25
## if the peak is not assigned find for the element having higher RSF to that BE value
NewElement<-NULL
energy <- peaks$table$BE[peakIndex]
NewElements <- FindElmtList(energy, DeltaEnergy, BE, ElmtList)
if (is.null(NewElements)){
idx<-max(which(object[[1]] > energy)) #find all elements > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
EE<-as.character(peaks$table$BE[peakIndex])
cat("\n Warning: No Element found at energy ", EE, " Please check Energy scale Alignment!")
}
EleTable<-rbind(EleTable, NewElements) #for a given energy a list of element falling in the range: energy-DEn, energy+DEn is produced
elmLbl<-rbind(elmLbl, NewElements) #here only the elements found nearby the energy value
if (is.null(elmLbl)) {
# do nothing!
} else {
idx<-max(which(object[[1]]> energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
##print LBL elementi trovati
Nrw<-nrow(elmLbl)
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Y boundaries
intensity <- Yrng[2] - Nrw*DeltaY #shift to lower y
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for(ii in 1:Nrw){
if (length(elmLbl)>0 && SpectrumType =="CoreLines"){
newlab <- paste(elmLbl[ii,"Element"], elmLbl[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(elmLbl)>0 && SpectrumType == "AugerTransitions") {
newlab <- paste(elmLbl[ii,"Element"], elmLbl[ii,"Transition"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow=FALSE
}
}
}
names(EleTable)<-c("Element", "Orbital", "BE", "KE", "RSF_K", "RSF_S")
return(EleTable)
}
#---Function to extract list of elements in a given energy interval
FindElmtList<-function(energy, DeltaEnergy, BE, ElmtList){
EleTable<-NULL
if (BE) {
Escale="BE"
} else {
Escale="KE"
}
ElmtList[,Escale] <- as.numeric(ElmtList[,Escale])
EleTable <- subset(ElmtList, ElmtList[,Escale] >= energy-DeltaEnergy) #extract all element with energy >= energy+DeltaEnergy
EleTable <- subset(EleTable, EleTable[,Escale] <= energy+DeltaEnergy) #from that list select those with energy <= energy+DeltaEnergy
if (nrow(EleTable) == 0){ EleTable<-NULL }
return(EleTable)
}
#--- find first element in list whose position is close to 'energy' less than DeltaEnergy
NearerElement <- function(energy, DeltaEnergy, object, ElmtList) {
energy<-as.numeric(energy)
BE<-FALSE #imposto KE
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-NULL
DEn = 0.3
while(is.null(EleTable)){
EleTable<-FindElmtList(energy, DEn, BE, ElmtList)
DEn <- DEn + 0.2
if (DEn > DeltaEnergy) {
cat("\n No elements found with the selected precision!")
break
}
}
idx<-max(which(object[[1]]> energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[1,"Element"], EleTable[1,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[1,"Element"], EleTable[1,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else {
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
}
if (!is.null(EleTable)) {
space<-data.frame(Element=" ", Orbital=" ", BE=" ", KE=" ", RSF_K=" ", RSF_S=" ")
EleTable<-rbind(EleTable, space)
}
return(EleTable)
}
#--- Check All elements which RSFmax distance is less than DeltaEnergy
CoreLinesMaxRSF <- function(energy, DeltaEnergy=3, object, ElmtList) { #, index=1
posLbl <- NULL
energy<-as.numeric(energy)
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-FindElmtList(energy, DeltaEnergy, BE, ElmtList)
if (object@Flags[3] == TRUE){
idx<-which(EleTable[ ,6] == max(EleTable[ ,6]), arr.ind = TRUE) #search for the max in the RSF column Scienta
} else {
idx<-which(EleTable[ ,5] == max(EleTable[ ,5]), arr.ind = TRUE) #search for the max in the RSF column Kratos
}
EleTable<-EleTable[idx,] #select the EleTable-row with max RSF
Nrw<-nrow(EleTable)
if (is.null(Nrw)) {
#--- object[[1]] $x values, object[[2]] $y values
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab)
} else if (Nrw > 0) {
ii=1
#--- If same element repeats itself in the EleTable only that wit max RSF is kept
while(ii < Nrw){ #cannot use a FOR-loop since it is not sensitive to Nrw changes
element<-EleTable[ii,1] #
RepIndx<-grep(element, EleTable[ ,1]) #how many times an element is present in the EleTable
MaxIndx<-which(EleTable[RepIndx,3]==max(EleTable[RepIndx,3]), arr.ind=TRUE) #select the max RSF among EleTable-rows
LL<-length(RepIndx) #N. rows of tmp
for (jj in LL:1){ #ATTENZIONE: regressive FOR because rows are cancelled from the EleTable
if (RepIndx[jj] != RepIndx[MaxIndx]){ #if the EleTable-row hasn't max RSF
EleTable<-EleTable[-RepIndx[jj], ] #drop the EleTable-row
Nrw<-Nrw-1
}
}
ii<-ii+1
}
Nrw<-nrow(EleTable)
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-object[[2]][idx]
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Ygraph boundaries
intensity <- Yrng[2] - Nrw*DeltaY
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for (ii in 1:Nrw){
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow=FALSE
}
}
return(EleTable)
}
#--- Find ANY element with energy
AllElements <- function(energy, DeltaEnergy=2, object, ElmtList) {
posLbl <- NULL
posY <- NULL
energy<-as.numeric(energy)
if (object@Flags[1]) { BE=TRUE } # energy scale is BINDING ENERGY
EleTable<-FindElmtList(energy, DeltaEnergy, BE, ElmtList)
Nrw<-nrow(EleTable)
if (is.null(Nrw)) {
idx<-max(which(object[[1]] > energy)) # which gives the index of all the elements of object$x > energy
intensity<-max(object[[2]][(idx-5):(idx+5)])
newlab<-"??"
DispLab(list(x=energy,y=intensity), label=newlab, arrow=TRUE, direction="right")
} else if (Nrw > 0) {
idx<-max(which(object[[1]] > energy))
intensity<-max(object[[2]][(idx-5):(idx+5)])
Yrng<-range(object[[2]])
DeltaY<-(Yrng[2]-Yrng[1])/20 #vertical shift to not superpose labels
if ((intensity+Nrw*DeltaY)>Yrng[2]){ #if TRUE => out of Ygraph boundaries
intensity <- Yrng[2] - Nrw*DeltaY
}
for (ii in 1:Nrw){
posLbl[ii]<-intensity+DeltaY*ii
}
arrow=TRUE
for (ii in 1:Nrw){
idx<-max(which(object[[1]] > energy))
intensity<-object[[2]][idx]
if (length(EleTable)>0 && names(ElmtList)[2] =="Orbital"){ #list of corelines was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Orbital"], sep="")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
} else if (length(EleTable)>0 && names(ElmtList)[2] == "Transitions") { #list of Auger Transitions was selected
newlab <- paste(EleTable[ii,"Element"], EleTable[ii,"Transition"], sep=" ")
newlab <- gsub(" ", "", newlab, fixed=TRUE) #drop white spaces
DispLab(list(x=energy,y=posLbl[ii]), label=newlab, arrow, direction="right", color="blue")
}
arrow<-FALSE
}
}
return(EleTable)
}
#--- prints the ElementTable in a formatted fashion
ShowTablePeaks <- function(EleTable, SpectrumType) {
if(SpectrumType == "CoreLines") { Wdth=10 }
if(SpectrumType == "AugerTransitions") { Wdth=12 }
cat("\n\n\n ***** IDENTIFIED ELEMENTS ***** \n")
LL<-nrow(EleTable)
sss<-format(names(EleTable), justify="right", width=Wdth)
cat("\n", sss)
for(ii in 1:LL){
sss<-as.character(gsub(" ", "", EleTable[ii, ], fixed=TRUE))
sss<-format(sss, justify="right", width=Wdth)
cat("\n",sss)
}
}
plotPeaks <- function(object, peaks=NULL, type = c("normal","corrected"), ...) {
if (is.null(peaks) ) stop("\npeaks is NULL")
type <- match.arg(type)
## plot curve
if (type == "normal") {
plot(object)
lines(object$x, peaks$baseline[1,], col=2) ## baseline
points(peaks$table$BE, peaks$table$orig, col=3, cex=1.0) ## peaks
} else {
plot(object$x, peaks$corrected[1,], type="l", xlim=rev(c(range(object$x))), xlab=object@units[1], ylab=object@units[2], main = object@Symbol )
points(peaks$table$BE, peaks$table$corr, col=3, cex=1.0) ## peaks
}
## Peaks Label
if ( ! all(is.na(names(peaks$table$BE)) ) ) {
for (PeakBEIndx in seq_along(peaks$table$BE)) {
if (type == "normal") {
DispLab(list(x=peaks$table$BE[PeakBEIndx],
y=peaks$table$orig[PeakBEIndx]),
label=names(peaks$table$BE[PeakBEIndx]),
arrow=TRUE,
direction="right",
...)
} else {
DispLab(list(x=peaks$table$BE[PeakBEIndx],
y=peaks$table$corr[PeakBEIndx]),
label=names(peaks$table$BE[PeakBEIndx]),
arrow=TRUE,
direction="right",
...)
}
}
}
}
DispLab <- function(position.list,
label,
color="blue",
arrow = TRUE,
xspanf = 1, yspanf = 3, lenarrow = 0.08,
direction = c("right", "left", "center"),
...) {
# position.list = list(x,y)
direction <- match.arg(direction)
X0 <- position.list$x
# orizontal segment xspanf % of xrange
xspan <- abs(par("usr")[2]-par("usr")[1]) * xspanf/100
# vertical segment 3% of yrange
yspan <- abs(par("usr")[4]-par("usr")[3]) * yspanf/100
Yspan <- rep(yspan, length(X0))
# reverse yspan if y+2*yspan > ymax
if (any((position.list$y + 2*yspan) > par("usr")[4])) {
Yspan[which((position.list$y + 2*yspan) > par("usr")[4])] <- -yspan
}
Y0 <- position.list$y + 2*Yspan
Y1 <- position.list$y + Yspan
Y2 <- position.list$y + 3*Yspan
# arrow from(x0,y0) to (x1,y1)
if (arrow) {
arrows(X0, Y0, X0, Y1, length = lenarrow, col = color)
switch(direction,
"right" = {
X1 <- X0 + xspan
#segments(X0,Y0, X1, Y0, col=color)
text(X1, Y0, labels = label, col=color, pos=4, offset=0.5, ...)## etichetta
},
"left" = {
X1 <- X0 - xspan
#segments(X0,Y0, X1, Y0, col=color)
text(X1, Y0, labels = label, col=color, pos=2, offset=0.5, ...)## etichetta
},
"center" = {
text(X0, Y0, labels = label, col=color, pos=3, offset=0.5, ...)## etichetta
}
)
}
else text(X0, Y0, labels = label, pos=4, col=color, ...)
}
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