R/Functions_peptides.R
In mjhelf/MassTools: R package for mass and molecular formula calculations
Defines functions
plotAnnotatedPeptide
permutatePeptideMass
countAAs
PeptideMF
Documented in
countAAs
PeptideMF
permutatePeptideMass
plotAnnotatedPeptide
#' @title PeptideMF
#'
#' convert peptide sequences into an MFobjects
#'
#' @param seq one or more peptide sequences in a character vector
#' @param AAs molecular formulas for each amino acid letter, defaults to proteinogenic amino acids
#'
#' @return a list of MFobjects
#'
#' @export
PeptideMF <- function(seq, AAs = c("A" = "C3H7NO2", "R" = "C6H14N4O2", "N" = "C4H8N2O3",
"D" = "C4H7NO4", "C" = "C3H7NO2S", "Q" = "C5H10N2O3",
"E" = "C5H9NO4", "G" = "C2H5NO2", "H" = "C6H9N3O2",
"I" = "C6H13NO2", "L" = "C6H13NO2", "K" = "C6H14N2O2",
"M" = "C5H11NO2S", "F" = "C9H11NO2", "P" = "C5H9NO2",
"S" = "C3H7NO3", "T" = "C4H9NO3", "W" = "C11H12N2O2",
"Y" = "C9H11NO3", "V" = "C5H11NO2")){
seq <- gsub("[[:space:]]","",seq)
pepAAs <- strsplit(seq, split = "")
Ecounts <- lapply(pepAAs, function(p){makeMF(paste0(paste(AAs[p], collapse = ""),paste(rep("H-2O-1",length(p)-1), collapse = "") ))})
return(Ecounts)
}
#' countAAs
#'
#' count amino acids in a sequence
#'
#' @param seq one or more peptide sequences in a character vector
#'
#' @return a list of named numeric vectors
#'
#' @export
countAAs <- function(seq){
seq <- gsub("[[:space:]]","",seq)
pepAAs <- strsplit(seq, split = "")
uniques <- lapply(pepAAs, unique)
res <- mapply(function(u,p){
counts <- sapply(u,function(aa){sum(p==aa)});
names(counts) <- u;
return(counts)},
uniques,pepAAs, SIMPLIFY = F)
return(res)
}
#' permutatePeptideMass
#'
#' Apply a set of mass modifications to a peptide with a known mass
#'
#' @param df data.frame with at least two columns, one with a non-empty
#' sequence string and one with a mass for that sequence
#' @param modifications a data.frame with colums \code{AAs}
#' @param sequenceCol name of the sequence column in df
#' @param massCol name of the mass column in df
#' @param chargeCol name of column that specifies charge state (used to adjust
#' modification masses)
#'
#' @details
#' \subsection{modifications}{
#' Columns that need to be in the \code{modifications data.frame}:
#' \describe{
#' \item{AAs}{containing letters for the amino acids (e.g. "TS")
#' affected by this modification}
#' \item{min}{minimum number of times this modification can be applied}
#' \item{max}{maximum number of times this modification can be applied}
#' \item{mass}{mass of this modification}
#' \item{tag}{ label for this modification (will automatically be preceded by
#' number of these modifications applied)}
#' }
#' min and max can be positive, negative or 0. The larger *absolute* value has
#' to be in the \code{max} column
#' }
#'
#' @examples
#' peptides = data.frame(seq = "ASDFGHKLIPYTREWQCNM",mz = 2295.056)
#' mods = data.frame(AAs = c("TS", ""),
#' min = c(0,1), max = c(-10,2),
#' mass = c(18.01,12.0), tag = c("DH","C") )
#'
#' permutatePeptideMass(peptides, mods)
#'
#'
#' @seealso \code{\link{permutateMass}}
#'
#' @export
permutatePeptideMass <- function(df, modifications,
sequenceCol = "seq",
massCol = "mz",
chargeCol = NULL){
if((missing(modifications)
|| is.null(modifications)
||!nrow(modifications))
){
if(!"modifications" %in% colnames(df)){
df$modifications <- ""
}
return(df)
}
res <- lapply(seq(nrow(df)),function(i, modifications){
AAcounts <- countAAs(df[[sequenceCol]][i])[[1]]
selective <- which(modifications$AAs != "" & !is.na(modifications$AAs))
if(length(selective) > 0){
selectivecounts <- sapply(selective,function(sel){
targets <- countAAs(modifications$AAs[sel])[[1]]
targetAAs <- match(names(targets), names(AAcounts))
if(!any(!is.na(targetAAs))){
return(0)
}
return(sum(AAcounts[na.omit(targetAAs)]))
})
#make sure the minimum and maximum values are in line with the number of required amino acids, and allow the numbers to be negative,as well
modifications$min[selective] <- sapply(seq(length(selective)),
function(i){ sign(modifications$min[selective][i]) * min(c(abs(modifications$min[selective][i]),
selectivecounts[i])) })
modifications$max[selective] <- sapply(seq(length(selective)),
function(i){ sign(modifications$max[selective][i]) * min(c(abs(modifications$max[selective][i]),
selectivecounts[i])) })
}
#this means that users HAVE to put the larger *absolute* value to into the max column
#would advise against mixing negative and positive values in min and max columns!
modifications <- modifications[abs(modifications$max) >= abs(modifications$min),]
#use charge state
if(!is.null(chargeCol)){
modifications$mass <- modifications$mass/df[[chargeCol]][i]
}
permutations <- permutateMass(df[[massCol]][i],modifications)
colnames(permutations)[colnames(permutations) == "mass"] <- massCol
suppressWarnings({
merged <- cbind(df[i, colnames(df) != massCol, drop = F], permutations)
})
return(merged)
}, modifications = modifications)
return(do.call(rbind,res))
}
#' plotAnnotatedPeptide
#'
#' plot an annotated peptide sequence
#'
#' @param peaklabels data.frame with labeling informationi,
#' as returned by \code{\link{annotateSpectrum}}
#' @param sequence peptide sequence (character)
#' @param parseLabels optionally apply parse() to
#' peaklabels$label and add as label (NYI)
#' @param sortby sort (decreasing) by this column. Only the top 2 ions
#' for each position (for both a,b,c ions AND x,y,z ions) will be shown
#' @param cx font size factor for the sequence characters,
#' other font sizes will be scaled accordingly
#' @param yoffset y axis offset
#'
#' @export
plotAnnotatedPeptide <- function(peaklabels,
sequence,
parseLabels = F,
sortby = "intensitySpec",
cx = 2,
yoffset = 0){
par(mar = c(0,0,0,0), xaxs = "i", yaxs = "i", xpd = NA)
chars <- strsplit(sequence, split = "")[[1]]
plot(numeric(),
numeric(),
ylim = c(-1,1),
xlim = c(0,1),
xaxs = "i", yaxs = "i",
type = "n", ann = FALSE, bty = "n",
axes = F#, asp =0.5
)
charheight <- strheight("M", cex = cx)
charwidth <- strwidth("M", cex = cx)
ionheight <- strheight("M", cex = 0.5*cx)
ionwidth <- strwidth("M", cex = 0.5*cx)
#this is now used as default, e.g. by strwidth() calls
par(cex = 0.5*cx)
spacer <- 0.45*ionheight
bigspacer <- 2*spacer
#conversionfactor between strheight and strwidth, assuming M is a square
#(tested M, and it is a square in terms of plotting dimensions)
HtoWratio <- charheight/charwidth
fieldwidth <- charwidth*1.02
centers <- (seq(length(chars))*fieldwidth-0.5*fieldwidth
+ (0.5-0.5*fieldwidth*length(chars)))
#last part centers sequence in plot area
bottoms <- -0.55*charheight + yoffset
tops <- 0.5*charheight + yoffset
bionpos <- tops + 0.5*charheight
yionpos <- bottoms - 0.5*charheight
text(centers,yoffset,labels=chars, cex=cx, adj=c(0.5,0.5))
if(nrow(peaklabels)>0){
if(sortby %in% colnames(peaklabels)){
peaklabels <- peaklabels[order(peaklabels[[sortby]],
decreasing = T),]
}
peaklabels$ppm <- ((peaklabels$mz-peaklabels$mzSpec)/peaklabels$mzSpec)*1e6
massionlabels <- format(round(peaklabels$mzSpec,5),
nsmall = 5, scientific = F)
massionlabels[peaklabels$z == 1] <- paste0(massionlabels[peaklabels$z == 1],
"^{+{}}")
massionlabels[peaklabels$z > 1] <- paste0(massionlabels[peaklabels$z > 1],
"^{",
peaklabels$z[peaklabels$z > 1],
"+{}}")
#adjust the y ion positions to same scale as b ions
peaklabels$pos[peaklabels$type %in% c("x","y","z")] <- length(chars) - peaklabels$pos[peaklabels$type %in% c("x","y","z")]
#for drawing the fragmentation lines
presentB <- unique(peaklabels$pos[peaklabels$type %in% c("a","b","c")])
presentY <- unique(peaklabels$pos[peaklabels$type %in% c("x","y","z")])
alllines <- unique(c(presentB,presentY))
#vertical lines
segments(centers[alllines]+0.5*fieldwidth,rep(bottoms,
length(alllines)),
centers[alllines]+0.5*fieldwidth,rep(tops,
length(alllines)),
col = "black", lty = "solid", lwd = 1)
segments(centers[presentB]+0.5*fieldwidth,rep(tops,
length(presentB)),
centers[presentB]+0.1*fieldwidth,rep(bionpos - 0.05*charheight,
length(presentB)),
col = "black", lty = "solid", lwd = 1)
segments(centers[presentY]+0.5*fieldwidth,rep(bottoms,
length(presentY)),
centers[presentY]+0.9*fieldwidth,rep(yionpos + 0.05*charheight,
length(presentY)),
col = "black", lty = "solid", lwd = 1)
#this way of selection treats only picks the first one AND treats
#a b c ions the same (as opposed to just !duplicated(peaklabels$ion)
bsel <- which(peaklabels$type %in% c("a","b","c"))
bsel <- bsel[!duplicated(peaklabels$pos[bsel])]
ysel <- which(peaklabels$type %in% c("x","y","z"))
ysel <- ysel[!duplicated(peaklabels$pos[ysel])]
if(parseLabels){
labelsfi <- parse(text = peaklabels$label)
}else{
labelsfi <- peaklabels$mz
}
parsedlabs <- parse(text = gsub("\\[\\]","",paste0('"[',
peaklabels$modifications,
']"')))
#now find the second ranking ions
if(length(bsel)>0){
bsel2 <- which(peaklabels$type %in% c("a","b","c"))
bsel2 <- bsel2[!bsel2 %in% bsel]
bsel2 <- bsel2[!duplicated(peaklabels$pos[bsel2])]
#label the b ions
text(centers[presentB],
rep(bionpos, length(bsel)),
labels = parse(text = paste0("b[",presentB,"]^{}")),
adj=c(0.5,0), srt=0, cex = 0.5*cx)
##First rank labels
### b ion modifications
bmodlabels <- parsedlabs[bsel]
bion1modpos <- bionpos + 1.55*ionheight
text(centers[peaklabels$pos[bsel]],
rep(bion1modpos, length(bsel)),
labels = bmodlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
#ppm labels
bppmpos <- (bion1modpos
+ bigspacer
+ max(strwidth(bmodlabels))*HtoWratio)
bppmlabels <- paste0("(",format(round(peaklabels$ppm,1)[bsel],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[bsel]],
rep(bppmpos, length(bsel)),
labels = bppmlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bmasspos <- (bppmpos
+ spacer
+ max(strwidth(bppmlabels))*HtoWratio)
bmasslabels <- parse(text = massionlabels[bsel])
text(centers[peaklabels$pos[bsel]],
rep(bmasspos, length(bsel)),
labels = bmasslabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
##Second rank labels
### b ion modifications
if(length(bsel2)){
bmodlabels <- parsedlabs[bsel2]
bion1modpos <- (bmasspos
+ bigspacer
+ max(strwidth(bmasslabels))*HtoWratio)
text(centers[peaklabels$pos[bsel2]],
rep(bion1modpos, length(bsel2)),
labels = bmodlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bppmpos <- (bion1modpos
+ bigspacer
+ max(strwidth(bmodlabels))*HtoWratio)
bppmlabels <- paste0("(",format(round(peaklabels$ppm,1)[bsel2],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[bsel2]],
rep(bppmpos, length(bsel2)),
labels = bppmlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bmasspos <- (bppmpos
+ spacer
+ max(strwidth(bppmlabels))*HtoWratio)
bmasslabels <- parse(text = massionlabels[bsel2])
text(centers[peaklabels$pos[bsel2]],
rep(bmasspos, length(bsel2)),
labels = bmasslabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
}
}
if(length(ysel)){
ysel2 <- which(peaklabels$type %in% c("x","y","z"))
ysel2 <- ysel2[!ysel2 %in% ysel]
ysel2 <- ysel2[!duplicated(peaklabels$pos[ysel2])]
#label the y ions
text(centers[presentY]+1*fieldwidth,
rep(yionpos, length(ysel)),
labels = parse(text = paste0("y[",
length(chars)-presentY,
"]^{}")),
adj=c(0.5,1), srt=0, cex = 0.5*cx)
### y ion modifications
ymodlabels <- parsedlabs[ysel]
yion1modpos <- yionpos - 1.5*ionheight
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(yion1modpos, length(ysel)),
labels = ymodlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
yppmpos <- (yion1modpos
- bigspacer
- max(strwidth(ymodlabels, cex = 0.5*cx))*HtoWratio)
yppmlabels <-paste0("(",format(round(peaklabels$ppm,1)[ysel],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(yppmpos, length(ysel)),
labels = yppmlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
ymasspos <- (yppmpos
- spacer
- max(strwidth(yppmlabels))*HtoWratio)
ymasslabels <- parse(text = massionlabels[ysel])
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(ymasspos, length(ysel)),
labels = ymasslabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
if(length(ysel2)){
ymodlabels <-parsedlabs[ysel2]
yion1modpos <- (ymasspos
- bigspacer
- max(strwidth(ymasslabels))*HtoWratio)
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(yion1modpos, length(ysel2)),
labels = ymodlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
yppmpos <- (yion1modpos
- bigspacer
- max(strwidth(ymodlabels))*HtoWratio)
yppmlabels <-paste0("(",format(round(peaklabels$ppm,1)[ysel2],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(yppmpos, length(ysel2)),
labels = yppmlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
ymasspos <- (yppmpos
- spacer
- max(strwidth(yppmlabels))*HtoWratio)
ymasslabels <- parse(text = massionlabels[ysel2])
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(ymasspos, length(ysel2)),
labels = ymasslabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
}
}
}
#make sure the custom cex in function doesn't interfere
par(cex = 1)
}
mjhelf/MassTools documentation built on Nov. 19, 2021, 2:38 a.m.
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Defines functions plotAnnotatedPeptide permutatePeptideMass countAAs PeptideMF
Documented in countAAs PeptideMF permutatePeptideMass plotAnnotatedPeptide
#' @title PeptideMF
#'
#' convert peptide sequences into an MFobjects
#'
#' @param seq one or more peptide sequences in a character vector
#' @param AAs molecular formulas for each amino acid letter, defaults to proteinogenic amino acids
#'
#' @return a list of MFobjects
#'
#' @export
PeptideMF <- function(seq, AAs = c("A" = "C3H7NO2", "R" = "C6H14N4O2", "N" = "C4H8N2O3",
"D" = "C4H7NO4", "C" = "C3H7NO2S", "Q" = "C5H10N2O3",
"E" = "C5H9NO4", "G" = "C2H5NO2", "H" = "C6H9N3O2",
"I" = "C6H13NO2", "L" = "C6H13NO2", "K" = "C6H14N2O2",
"M" = "C5H11NO2S", "F" = "C9H11NO2", "P" = "C5H9NO2",
"S" = "C3H7NO3", "T" = "C4H9NO3", "W" = "C11H12N2O2",
"Y" = "C9H11NO3", "V" = "C5H11NO2")){
seq <- gsub("[[:space:]]","",seq)
pepAAs <- strsplit(seq, split = "")
Ecounts <- lapply(pepAAs, function(p){makeMF(paste0(paste(AAs[p], collapse = ""),paste(rep("H-2O-1",length(p)-1), collapse = "") ))})
return(Ecounts)
}
#' countAAs
#'
#' count amino acids in a sequence
#'
#' @param seq one or more peptide sequences in a character vector
#'
#' @return a list of named numeric vectors
#'
#' @export
countAAs <- function(seq){
seq <- gsub("[[:space:]]","",seq)
pepAAs <- strsplit(seq, split = "")
uniques <- lapply(pepAAs, unique)
res <- mapply(function(u,p){
counts <- sapply(u,function(aa){sum(p==aa)});
names(counts) <- u;
return(counts)},
uniques,pepAAs, SIMPLIFY = F)
return(res)
}
#' permutatePeptideMass
#'
#' Apply a set of mass modifications to a peptide with a known mass
#'
#' @param df data.frame with at least two columns, one with a non-empty
#' sequence string and one with a mass for that sequence
#' @param modifications a data.frame with colums \code{AAs}
#' @param sequenceCol name of the sequence column in df
#' @param massCol name of the mass column in df
#' @param chargeCol name of column that specifies charge state (used to adjust
#' modification masses)
#'
#' @details
#' \subsection{modifications}{
#' Columns that need to be in the \code{modifications data.frame}:
#' \describe{
#' \item{AAs}{containing letters for the amino acids (e.g. "TS")
#' affected by this modification}
#' \item{min}{minimum number of times this modification can be applied}
#' \item{max}{maximum number of times this modification can be applied}
#' \item{mass}{mass of this modification}
#' \item{tag}{ label for this modification (will automatically be preceded by
#' number of these modifications applied)}
#' }
#' min and max can be positive, negative or 0. The larger *absolute* value has
#' to be in the \code{max} column
#' }
#'
#' @examples
#' peptides = data.frame(seq = "ASDFGHKLIPYTREWQCNM",mz = 2295.056)
#' mods = data.frame(AAs = c("TS", ""),
#' min = c(0,1), max = c(-10,2),
#' mass = c(18.01,12.0), tag = c("DH","C") )
#'
#' permutatePeptideMass(peptides, mods)
#'
#'
#' @seealso \code{\link{permutateMass}}
#'
#' @export
permutatePeptideMass <- function(df, modifications,
sequenceCol = "seq",
massCol = "mz",
chargeCol = NULL){
if((missing(modifications)
|| is.null(modifications)
||!nrow(modifications))
){
if(!"modifications" %in% colnames(df)){
df$modifications <- ""
}
return(df)
}
res <- lapply(seq(nrow(df)),function(i, modifications){
AAcounts <- countAAs(df[[sequenceCol]][i])[[1]]
selective <- which(modifications$AAs != "" & !is.na(modifications$AAs))
if(length(selective) > 0){
selectivecounts <- sapply(selective,function(sel){
targets <- countAAs(modifications$AAs[sel])[[1]]
targetAAs <- match(names(targets), names(AAcounts))
if(!any(!is.na(targetAAs))){
return(0)
}
return(sum(AAcounts[na.omit(targetAAs)]))
})
#make sure the minimum and maximum values are in line with the number of required amino acids, and allow the numbers to be negative,as well
modifications$min[selective] <- sapply(seq(length(selective)),
function(i){ sign(modifications$min[selective][i]) * min(c(abs(modifications$min[selective][i]),
selectivecounts[i])) })
modifications$max[selective] <- sapply(seq(length(selective)),
function(i){ sign(modifications$max[selective][i]) * min(c(abs(modifications$max[selective][i]),
selectivecounts[i])) })
}
#this means that users HAVE to put the larger *absolute* value to into the max column
#would advise against mixing negative and positive values in min and max columns!
modifications <- modifications[abs(modifications$max) >= abs(modifications$min),]
#use charge state
if(!is.null(chargeCol)){
modifications$mass <- modifications$mass/df[[chargeCol]][i]
}
permutations <- permutateMass(df[[massCol]][i],modifications)
colnames(permutations)[colnames(permutations) == "mass"] <- massCol
suppressWarnings({
merged <- cbind(df[i, colnames(df) != massCol, drop = F], permutations)
})
return(merged)
}, modifications = modifications)
return(do.call(rbind,res))
}
#' plotAnnotatedPeptide
#'
#' plot an annotated peptide sequence
#'
#' @param peaklabels data.frame with labeling informationi,
#' as returned by \code{\link{annotateSpectrum}}
#' @param sequence peptide sequence (character)
#' @param parseLabels optionally apply parse() to
#' peaklabels$label and add as label (NYI)
#' @param sortby sort (decreasing) by this column. Only the top 2 ions
#' for each position (for both a,b,c ions AND x,y,z ions) will be shown
#' @param cx font size factor for the sequence characters,
#' other font sizes will be scaled accordingly
#' @param yoffset y axis offset
#'
#' @export
plotAnnotatedPeptide <- function(peaklabels,
sequence,
parseLabels = F,
sortby = "intensitySpec",
cx = 2,
yoffset = 0){
par(mar = c(0,0,0,0), xaxs = "i", yaxs = "i", xpd = NA)
chars <- strsplit(sequence, split = "")[[1]]
plot(numeric(),
numeric(),
ylim = c(-1,1),
xlim = c(0,1),
xaxs = "i", yaxs = "i",
type = "n", ann = FALSE, bty = "n",
axes = F#, asp =0.5
)
charheight <- strheight("M", cex = cx)
charwidth <- strwidth("M", cex = cx)
ionheight <- strheight("M", cex = 0.5*cx)
ionwidth <- strwidth("M", cex = 0.5*cx)
#this is now used as default, e.g. by strwidth() calls
par(cex = 0.5*cx)
spacer <- 0.45*ionheight
bigspacer <- 2*spacer
#conversionfactor between strheight and strwidth, assuming M is a square
#(tested M, and it is a square in terms of plotting dimensions)
HtoWratio <- charheight/charwidth
fieldwidth <- charwidth*1.02
centers <- (seq(length(chars))*fieldwidth-0.5*fieldwidth
+ (0.5-0.5*fieldwidth*length(chars)))
#last part centers sequence in plot area
bottoms <- -0.55*charheight + yoffset
tops <- 0.5*charheight + yoffset
bionpos <- tops + 0.5*charheight
yionpos <- bottoms - 0.5*charheight
text(centers,yoffset,labels=chars, cex=cx, adj=c(0.5,0.5))
if(nrow(peaklabels)>0){
if(sortby %in% colnames(peaklabels)){
peaklabels <- peaklabels[order(peaklabels[[sortby]],
decreasing = T),]
}
peaklabels$ppm <- ((peaklabels$mz-peaklabels$mzSpec)/peaklabels$mzSpec)*1e6
massionlabels <- format(round(peaklabels$mzSpec,5),
nsmall = 5, scientific = F)
massionlabels[peaklabels$z == 1] <- paste0(massionlabels[peaklabels$z == 1],
"^{+{}}")
massionlabels[peaklabels$z > 1] <- paste0(massionlabels[peaklabels$z > 1],
"^{",
peaklabels$z[peaklabels$z > 1],
"+{}}")
#adjust the y ion positions to same scale as b ions
peaklabels$pos[peaklabels$type %in% c("x","y","z")] <- length(chars) - peaklabels$pos[peaklabels$type %in% c("x","y","z")]
#for drawing the fragmentation lines
presentB <- unique(peaklabels$pos[peaklabels$type %in% c("a","b","c")])
presentY <- unique(peaklabels$pos[peaklabels$type %in% c("x","y","z")])
alllines <- unique(c(presentB,presentY))
#vertical lines
segments(centers[alllines]+0.5*fieldwidth,rep(bottoms,
length(alllines)),
centers[alllines]+0.5*fieldwidth,rep(tops,
length(alllines)),
col = "black", lty = "solid", lwd = 1)
segments(centers[presentB]+0.5*fieldwidth,rep(tops,
length(presentB)),
centers[presentB]+0.1*fieldwidth,rep(bionpos - 0.05*charheight,
length(presentB)),
col = "black", lty = "solid", lwd = 1)
segments(centers[presentY]+0.5*fieldwidth,rep(bottoms,
length(presentY)),
centers[presentY]+0.9*fieldwidth,rep(yionpos + 0.05*charheight,
length(presentY)),
col = "black", lty = "solid", lwd = 1)
#this way of selection treats only picks the first one AND treats
#a b c ions the same (as opposed to just !duplicated(peaklabels$ion)
bsel <- which(peaklabels$type %in% c("a","b","c"))
bsel <- bsel[!duplicated(peaklabels$pos[bsel])]
ysel <- which(peaklabels$type %in% c("x","y","z"))
ysel <- ysel[!duplicated(peaklabels$pos[ysel])]
if(parseLabels){
labelsfi <- parse(text = peaklabels$label)
}else{
labelsfi <- peaklabels$mz
}
parsedlabs <- parse(text = gsub("\\[\\]","",paste0('"[',
peaklabels$modifications,
']"')))
#now find the second ranking ions
if(length(bsel)>0){
bsel2 <- which(peaklabels$type %in% c("a","b","c"))
bsel2 <- bsel2[!bsel2 %in% bsel]
bsel2 <- bsel2[!duplicated(peaklabels$pos[bsel2])]
#label the b ions
text(centers[presentB],
rep(bionpos, length(bsel)),
labels = parse(text = paste0("b[",presentB,"]^{}")),
adj=c(0.5,0), srt=0, cex = 0.5*cx)
##First rank labels
### b ion modifications
bmodlabels <- parsedlabs[bsel]
bion1modpos <- bionpos + 1.55*ionheight
text(centers[peaklabels$pos[bsel]],
rep(bion1modpos, length(bsel)),
labels = bmodlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
#ppm labels
bppmpos <- (bion1modpos
+ bigspacer
+ max(strwidth(bmodlabels))*HtoWratio)
bppmlabels <- paste0("(",format(round(peaklabels$ppm,1)[bsel],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[bsel]],
rep(bppmpos, length(bsel)),
labels = bppmlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bmasspos <- (bppmpos
+ spacer
+ max(strwidth(bppmlabels))*HtoWratio)
bmasslabels <- parse(text = massionlabels[bsel])
text(centers[peaklabels$pos[bsel]],
rep(bmasspos, length(bsel)),
labels = bmasslabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
##Second rank labels
### b ion modifications
if(length(bsel2)){
bmodlabels <- parsedlabs[bsel2]
bion1modpos <- (bmasspos
+ bigspacer
+ max(strwidth(bmasslabels))*HtoWratio)
text(centers[peaklabels$pos[bsel2]],
rep(bion1modpos, length(bsel2)),
labels = bmodlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bppmpos <- (bion1modpos
+ bigspacer
+ max(strwidth(bmodlabels))*HtoWratio)
bppmlabels <- paste0("(",format(round(peaklabels$ppm,1)[bsel2],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[bsel2]],
rep(bppmpos, length(bsel2)),
labels = bppmlabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
bmasspos <- (bppmpos
+ spacer
+ max(strwidth(bppmlabels))*HtoWratio)
bmasslabels <- parse(text = massionlabels[bsel2])
text(centers[peaklabels$pos[bsel2]],
rep(bmasspos, length(bsel2)),
labels = bmasslabels,
adj=c(1,0.5), srt=270, cex = 0.5*cx)
}
}
if(length(ysel)){
ysel2 <- which(peaklabels$type %in% c("x","y","z"))
ysel2 <- ysel2[!ysel2 %in% ysel]
ysel2 <- ysel2[!duplicated(peaklabels$pos[ysel2])]
#label the y ions
text(centers[presentY]+1*fieldwidth,
rep(yionpos, length(ysel)),
labels = parse(text = paste0("y[",
length(chars)-presentY,
"]^{}")),
adj=c(0.5,1), srt=0, cex = 0.5*cx)
### y ion modifications
ymodlabels <- parsedlabs[ysel]
yion1modpos <- yionpos - 1.5*ionheight
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(yion1modpos, length(ysel)),
labels = ymodlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
yppmpos <- (yion1modpos
- bigspacer
- max(strwidth(ymodlabels, cex = 0.5*cx))*HtoWratio)
yppmlabels <-paste0("(",format(round(peaklabels$ppm,1)[ysel],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(yppmpos, length(ysel)),
labels = yppmlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
ymasspos <- (yppmpos
- spacer
- max(strwidth(yppmlabels))*HtoWratio)
ymasslabels <- parse(text = massionlabels[ysel])
text(centers[peaklabels$pos[ysel]]+fieldwidth,
rep(ymasspos, length(ysel)),
labels = ymasslabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
if(length(ysel2)){
ymodlabels <-parsedlabs[ysel2]
yion1modpos <- (ymasspos
- bigspacer
- max(strwidth(ymasslabels))*HtoWratio)
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(yion1modpos, length(ysel2)),
labels = ymodlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
yppmpos <- (yion1modpos
- bigspacer
- max(strwidth(ymodlabels))*HtoWratio)
yppmlabels <-paste0("(",format(round(peaklabels$ppm,1)[ysel2],
nsmall = 1, scientific = F),")")
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(yppmpos, length(ysel2)),
labels = yppmlabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
ymasspos <- (yppmpos
- spacer
- max(strwidth(yppmlabels))*HtoWratio)
ymasslabels <- parse(text = massionlabels[ysel2])
text(centers[peaklabels$pos[ysel2]]+fieldwidth,
rep(ymasspos, length(ysel2)),
labels = ymasslabels,
adj=c(1,0.5), srt=90, cex = 0.5*cx)
}
}
}
#make sure the custom cex in function doesn't interfere
par(cex = 1)
}
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