R/PeakML.Isotope.plotSamples.R
In andzajan/mzmatch.R: mzmatch and PeakML integration for XCMS.
Defines functions
PeakML.Isotope.plotSamples
Documented in
PeakML.Isotope.plotSamples
PeakML.Isotope.plotSamples <- function(isotopeChroms, metName, metFormula, metMass, metComment, stdRT, sampleType, sampleGroups, plotOrder, useArea, followCarbon, label, exclude_from_plots){
cat (exclude_from_plots)
cat("\n")
element <- substr(label,1,1)
if(is.null(stdRT)) stdRT <- NA
# grads <- c("black",
#rgb(0.750,0.700,1.000), rgb(0.400,0.320,0.800), rgb(0.150,0.060,0.600),
#rgb(0.700,0.900,1.000), rgb(0.320,0.640,0.800), rgb(0.060,0.420,0.600),
#rgb(0.900,1.000,0.700), rgb(0.640,0.800,0.320), rgb(0.420,0.600,0.060),
#rgb(1.000,0.850,0.700), rgb(0.800,0.560,0.320), rgb(0.600,0.330,0.060),
#rgb(1.000,0.700,0.700), rgb(0.800,0.320,0.320), rgb(0.600,0.060,0.060)
# )
# cbp <- c("black", "#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99", "#E31A1C", "#FDBF6F","#FF7F00", "#CAB2D6", "#6A3D9A", "#FFFF99", "#B15928")
cbp <- c("#666666", "#1F78B4", "#6A3D9A", "#33A02C", "#B15928", "#FF7F00", "#E31A1C", "#A6CEE3", "#CAB2D6", "#B2DF8A", "#FFFF99", "#FDBF6F", "#FB9A99")
# dist_grads <- c("black", rgb(1.000,0.750,0.500), rgb(1.000,0.500,0.000), rgb(1.000,1.000,0.600), rgb(0.700,1.000,0.550), rgb(0.200,1.000,0.000), rgb(0.650,0.930,1.000), rgb(0.100,0.700,1.000), rgb(0.800,0.750,1.000), rgb(0.400,0.300,1.000), rgb(1.000,0.600,0.750), rgb(1.000,1.000,0.200), rgb(0.900,0.100,0.200))
clrs <- cbp
numClrs <- length(clrs)
axExFact <-1.1 # This is a buffer to get the y axis of the bar plots right
par(oma=c(0,0,0,0))
processRatioMtx <- function(ratioMtx){
plotMtx <- matrix(nrow=nrow(ratioMtx), ncol=ncol(ratioMtx))
rownames(plotMtx) <- row.names(ratioMtx)
for (r in 1:nrow(ratioMtx)){
sumr <- sum(ratioMtx[r,])
for (c in 1:ncol(ratioMtx)){
if (!is.na(ratioMtx[r,c])) {
plotMtx[r,c] <- ratioMtx[r,c]/sumr
} else {
plotMtx[r,c] <- 0
}
}
}
plotMtx
}
mzList <- isotopeChroms[[1]]
intList <- isotopeChroms[[2]]
rtList <- isotopeChroms[[3]]
numPeakGroups <- length(mzList)
numSampleGroups <- length(mzList[[1]])
numCarbons <- length(mzList[[1]][[1]])
#numReplicates <- length(mzList[[1]][[1]][[1]])
metName <- unlist(strsplit(as.character(metName), ", "))
fillLabels <- c("UL" , paste(as.character("+"),c(1:numCarbons),sep=""))# create a list of isotop names
fillColor <- clrs[1:numCarbons]
if (numCarbons > numClrs) {
n = numCarbons - numClrs
rainClrs <- rainbow(n, s = 1, v = 1, start = 0, end = max(1,n - 1)/n, alpha = 1)
fillColor <- c(clrs, rainClrs)
}
if (followCarbon > numCarbons){
followCarbon <- numCarbons
}
for (peakGroup in 1:numPeakGroups){
trendList <- PeakML.Isotope.getTrendList (intList, sampleGroups, useArea) [[peakGroup]]
ratioMtx <- processRatioMtx (t(PeakML.Isotope.getRatioMtxList (intList, sampleGroups, useArea, metName[1]) [[peakGroup]]))
par (mar=c(0,0,0,0))
plot (c(1:10), c(1:10), xlab="", ylab="", pch="", axes=F)
if(length(metName)==1){
text(1.5, 6, metName[1], cex = 2, pos=4)
text(1.5, 4, paste("Formula:", metFormula, metComment, "Mass:", round(metMass,3), "Std.RT:", stdRT, "Ion:", sampleType, sep = " "), pos=4, cex = 1.5)
# text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, sep = " "), pos=4, cex = 1.5)
} else {
text(1.5, 7, metName[1], cex = 2, pos=4)
text(1.5, 5, paste(metName[2:length(metName)], collapse=","), cex = .5, pos=4)
text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, "Ion:", sampleType, sep = " "), pos=4, cex = 1)
# text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, sep = " "), pos=4, cex = 1)
}
legend(1.5, 3, fill=fillColor, fillLabels[1:numCarbons], bty="n", horiz=TRUE, x.intersp=.1)
plot (1, 1, xlab="", ylab="", pch="", axes=F)
text(1, 1, paste("G", as.character(peakGroup), sep=""), cex = 3)
for (item in 1:length(plotOrder)){
if(plotOrder[item] == "LEGEND"){
#par(mar=c(0.5,0.5,0.5,0.5))
par (mar=c(0,0,0,0))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
legend("topleft",fill=fillColor, fillLabels[1:numCarbons], bty="n")
} else if (plotOrder[item] == "TREND"){
errBar <- function(x, y, upper, lower=upper, length=0.1,...){
if(length(x) != length(y) | length(y) !=length(lower) | length(lower) != length(upper))
stop("vectors must be same length")
arrows(x, y+upper, x, y-lower, angle=90, code=3, length=length, ...)
}
trendMtx <- PeakML.Isotope.getTrendMtx(trendList, sampleGroups)
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(trendMtx))
trendMtx <-subset(trendMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
# if(!is.null(exclude_from_plots)){
# exclude <- which(sampleGroups %in% exclude_from_plots)
# trendMtx <- trendMtx[,- exclude]
# lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
#
# }
trendMtx.sum <- apply(trendMtx, 2, sum)
trendMtx.sd <- apply(trendMtx, 2, sd)
ylimit <- sum(max(trendMtx.sum), max(trendMtx.sd))
# calculate std err
#errMtx <- replace(trendMtx, trendMtx==0, NA)
#stdErr <- apply(errMtx, 2, PeakML.Methods.getStdErr)
#par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
if (useArea == FALSE){
#ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "mean peak height"
} else {
#ylabel <- paste(metName[1], "(mean peak area)", sep= " ")
ylabel <- "mean peak area"
}
mp<-barplot(trendMtx, beside=FALSE, col=fillColor, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = colnames(trendMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
errBar(mp, trendMtx.sum, trendMtx.sd/numCarbons, lwd=.3)
title("Trend plot", cex.main=0.8)
axis(2)
} else if (plotOrder[item] == "LABELLED"){
if(is.na(followCarbon)) followCarbon <- 2
if (followCarbon == 2){
fcMtx <-PeakML.Isotope.getFCMtxAbun(trendList, sampleGroups, followCarbon, element)
#fcMtx <-PeakML.Isotope.getFCMtxAbun(trendList, sg, followCarbon, element)
} else {
fcMtx <- PeakML.Isotope.getFCMtx(trendList, sampleGroups, followCarbon)
#fcMtx <- PeakML.Isotope.getFCMtx(trendList, sg, followCarbon)
}
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(fcMtx))
fcMtx <-subset(fcMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
if (useArea == FALSE){
# ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "mean peak height"
} else {
# ylabel <- paste(metName[1], "(mean peak area)", sep= " ")
ylabel <- "mean peak area"
}
ylimit <- max(apply(fcMtx, 2, sum)) * axExFact
if (!ylimit==0){
# par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
if (followCarbon==2){
overlap <- "#993399" # expected NA / NA whichever is smaller
expectedLarger <- "#FF9988" # expected natuabun is greater
measuredLarger <- "#8877FF" # blue
colvector <- c(overlap, expectedLarger, measuredLarger)
} else {
colvector <- fillColor[followCarbon]
}
# barplot(fcMtx, beside=FALSE, col=colvector, axisnames=FALSE, ylab=ylabel, ylim=c(0,ylimit), border=NA)
# axis(1, las=3, at=c(1:length(sampleGroups)), labels=sampleGroups, lwd=0, cex.axis=.8)
mp<-barplot(fcMtx, beside=FALSE, col=colvector, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = colnames(fcMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
# axis(1, at = mp, labels = FALSE)
title(paste("Trend of ", followCarbon-1,"", element, " labelled isotopomer"), cex.main=0.8)
#title(paste("Trend of natural abundance (", element, ")"), cex.main=0.8)
axis(2)
if (followCarbon==2){
legend("topright",fill=colvector, c("Overlap", "<Expected", ">Expected"), bty="n")
}
} else {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(0.5,0.5,0.5,0.5))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
}
} else if (plotOrder[item] == "RATIO") {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
mp<-barplot(t(ratioMtx), beside=FALSE, col=fillColor, ylab="% area under peak", ylim = c(0,1), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = row.names(ratioMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.2)
# axis(1, at = mp, labels = FALSE)
title("Ratio", cex.main=0.8)
axis(2)
} else if (plotOrder[item] == "TOTRATIO") {
getRelAbunMtx <- function (trendList, sampleGroups, followCarbon){
numCarbons <- length(trendList[[1]])
plotMtx <- matrix(nrow = 1, ncol = length(sampleGroups))
dimnames(plotMtx) <- list(c("RelAbun"), sampleGroups)
for (sam in 1:length(sampleGroups)){
for (row in 1:length(rownames(plotMtx))){
x <- trendList[[sam]][[followCarbon]]
y <- sum(unlist(trendList[[sam]]))
if (is.null(x)){
x <- 0
}
if (is.null(y)){
y <- 0
}
plotMtx[row, sam] <- x/y*100
}
}
plotMtx
}
if(is.na(followCarbon)) followCarbon <- 2
ftMtx <- getRelAbunMtx(trendList, sampleGroups, followCarbon)
ftMtx[is.nan(ftMtx)] <- 0
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(ftMtx))
ftMtx <-subset(ftMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
if (useArea == FALSE){
# ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "% relative labelling"
} else {
ylabel <- "% relative labelling"
#ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
}
ylimit <- max(apply(ftMtx, 2, sum)) * axExFact
if (ylimit>100) ylimit <- 100
# if (is.nan(ylimit)){ylimit<-0}
if (!ylimit==0){
# par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
colvector <- fillColor[followCarbon]
mp<-barplot(ftMtx, beside=FALSE, col=colvector, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels=colnames(ftMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
# axis(1, at = mp, labels = FALSE)
title("Relative labelling pattern", cex.main=0.8)
axis(2)
} else {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(0.5,0.5,0.5,0.5))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
}
} else if (plotOrder[item] == "EMPTY"){
# This is a an empty plot for flexibility e.g. define empty if a plot is not needed
plot (1, 1, xlab="", ylab="", pch="", axes=F)
} else{
if (! length(unlist(rtList[[peakGroup]][[item]])) == 0){
maxRT <- max(unlist(rtList[[peakGroup]][[item]]),na.rm=TRUE)
minRT <- min(unlist(rtList[[peakGroup]][[item]]),na.rm=TRUE)
maxIN <- max(unlist(intList[[peakGroup]][[item]]),na.rm=TRUE)
minIN <- 0
}else{
maxRT <- 0
minRT <- 0
maxIN <- 0
minIN <- 0
}
# par(mar=c(4,4,0.5,0.5), mgp=c(1.5,0.5,0))
par(mar=c(2,2,1,0), mgp=c(0.5,0.5,0))
plot (1, 1, pch="", xlab="", ylab="", xlim=c(minRT,maxRT), ylim=c(minIN,maxIN), cex.axis=0.75)
for (isotop in 1:numCarbons){
numReplicates <- length(rtList[[peakGroup]][[item]][[isotop]])
for (rep in 1:numReplicates){
points(rtList[[peakGroup]][[item]][[isotop]][[rep]], intList[[peakGroup]][[item]][[isotop]][[rep]], type="l",col=fillColor[[isotop]])
}
}
legend("topright", plotOrder[item], bty="n", cex=.5)
}
}
}
}
andzajan/mzmatch.R documentation built on Dec. 1, 2020, 11:33 a.m.
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Defines functions PeakML.Isotope.plotSamples
Documented in PeakML.Isotope.plotSamples
PeakML.Isotope.plotSamples <- function(isotopeChroms, metName, metFormula, metMass, metComment, stdRT, sampleType, sampleGroups, plotOrder, useArea, followCarbon, label, exclude_from_plots){
cat (exclude_from_plots)
cat("\n")
element <- substr(label,1,1)
if(is.null(stdRT)) stdRT <- NA
# grads <- c("black",
#rgb(0.750,0.700,1.000), rgb(0.400,0.320,0.800), rgb(0.150,0.060,0.600),
#rgb(0.700,0.900,1.000), rgb(0.320,0.640,0.800), rgb(0.060,0.420,0.600),
#rgb(0.900,1.000,0.700), rgb(0.640,0.800,0.320), rgb(0.420,0.600,0.060),
#rgb(1.000,0.850,0.700), rgb(0.800,0.560,0.320), rgb(0.600,0.330,0.060),
#rgb(1.000,0.700,0.700), rgb(0.800,0.320,0.320), rgb(0.600,0.060,0.060)
# )
# cbp <- c("black", "#A6CEE3", "#1F78B4", "#B2DF8A", "#33A02C", "#FB9A99", "#E31A1C", "#FDBF6F","#FF7F00", "#CAB2D6", "#6A3D9A", "#FFFF99", "#B15928")
cbp <- c("#666666", "#1F78B4", "#6A3D9A", "#33A02C", "#B15928", "#FF7F00", "#E31A1C", "#A6CEE3", "#CAB2D6", "#B2DF8A", "#FFFF99", "#FDBF6F", "#FB9A99")
# dist_grads <- c("black", rgb(1.000,0.750,0.500), rgb(1.000,0.500,0.000), rgb(1.000,1.000,0.600), rgb(0.700,1.000,0.550), rgb(0.200,1.000,0.000), rgb(0.650,0.930,1.000), rgb(0.100,0.700,1.000), rgb(0.800,0.750,1.000), rgb(0.400,0.300,1.000), rgb(1.000,0.600,0.750), rgb(1.000,1.000,0.200), rgb(0.900,0.100,0.200))
clrs <- cbp
numClrs <- length(clrs)
axExFact <-1.1 # This is a buffer to get the y axis of the bar plots right
par(oma=c(0,0,0,0))
processRatioMtx <- function(ratioMtx){
plotMtx <- matrix(nrow=nrow(ratioMtx), ncol=ncol(ratioMtx))
rownames(plotMtx) <- row.names(ratioMtx)
for (r in 1:nrow(ratioMtx)){
sumr <- sum(ratioMtx[r,])
for (c in 1:ncol(ratioMtx)){
if (!is.na(ratioMtx[r,c])) {
plotMtx[r,c] <- ratioMtx[r,c]/sumr
} else {
plotMtx[r,c] <- 0
}
}
}
plotMtx
}
mzList <- isotopeChroms[[1]]
intList <- isotopeChroms[[2]]
rtList <- isotopeChroms[[3]]
numPeakGroups <- length(mzList)
numSampleGroups <- length(mzList[[1]])
numCarbons <- length(mzList[[1]][[1]])
#numReplicates <- length(mzList[[1]][[1]][[1]])
metName <- unlist(strsplit(as.character(metName), ", "))
fillLabels <- c("UL" , paste(as.character("+"),c(1:numCarbons),sep=""))# create a list of isotop names
fillColor <- clrs[1:numCarbons]
if (numCarbons > numClrs) {
n = numCarbons - numClrs
rainClrs <- rainbow(n, s = 1, v = 1, start = 0, end = max(1,n - 1)/n, alpha = 1)
fillColor <- c(clrs, rainClrs)
}
if (followCarbon > numCarbons){
followCarbon <- numCarbons
}
for (peakGroup in 1:numPeakGroups){
trendList <- PeakML.Isotope.getTrendList (intList, sampleGroups, useArea) [[peakGroup]]
ratioMtx <- processRatioMtx (t(PeakML.Isotope.getRatioMtxList (intList, sampleGroups, useArea, metName[1]) [[peakGroup]]))
par (mar=c(0,0,0,0))
plot (c(1:10), c(1:10), xlab="", ylab="", pch="", axes=F)
if(length(metName)==1){
text(1.5, 6, metName[1], cex = 2, pos=4)
text(1.5, 4, paste("Formula:", metFormula, metComment, "Mass:", round(metMass,3), "Std.RT:", stdRT, "Ion:", sampleType, sep = " "), pos=4, cex = 1.5)
# text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, sep = " "), pos=4, cex = 1.5)
} else {
text(1.5, 7, metName[1], cex = 2, pos=4)
text(1.5, 5, paste(metName[2:length(metName)], collapse=","), cex = .5, pos=4)
text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, "Ion:", sampleType, sep = " "), pos=4, cex = 1)
# text(1.5, 4, paste("Formula:", metFormula, "Mass:", round(metMass,3), "Std.RT:", stdRT, sep = " "), pos=4, cex = 1)
}
legend(1.5, 3, fill=fillColor, fillLabels[1:numCarbons], bty="n", horiz=TRUE, x.intersp=.1)
plot (1, 1, xlab="", ylab="", pch="", axes=F)
text(1, 1, paste("G", as.character(peakGroup), sep=""), cex = 3)
for (item in 1:length(plotOrder)){
if(plotOrder[item] == "LEGEND"){
#par(mar=c(0.5,0.5,0.5,0.5))
par (mar=c(0,0,0,0))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
legend("topleft",fill=fillColor, fillLabels[1:numCarbons], bty="n")
} else if (plotOrder[item] == "TREND"){
errBar <- function(x, y, upper, lower=upper, length=0.1,...){
if(length(x) != length(y) | length(y) !=length(lower) | length(lower) != length(upper))
stop("vectors must be same length")
arrows(x, y+upper, x, y-lower, angle=90, code=3, length=length, ...)
}
trendMtx <- PeakML.Isotope.getTrendMtx(trendList, sampleGroups)
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(trendMtx))
trendMtx <-subset(trendMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
# if(!is.null(exclude_from_plots)){
# exclude <- which(sampleGroups %in% exclude_from_plots)
# trendMtx <- trendMtx[,- exclude]
# lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
#
# }
trendMtx.sum <- apply(trendMtx, 2, sum)
trendMtx.sd <- apply(trendMtx, 2, sd)
ylimit <- sum(max(trendMtx.sum), max(trendMtx.sd))
# calculate std err
#errMtx <- replace(trendMtx, trendMtx==0, NA)
#stdErr <- apply(errMtx, 2, PeakML.Methods.getStdErr)
#par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
if (useArea == FALSE){
#ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "mean peak height"
} else {
#ylabel <- paste(metName[1], "(mean peak area)", sep= " ")
ylabel <- "mean peak area"
}
mp<-barplot(trendMtx, beside=FALSE, col=fillColor, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = colnames(trendMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
errBar(mp, trendMtx.sum, trendMtx.sd/numCarbons, lwd=.3)
title("Trend plot", cex.main=0.8)
axis(2)
} else if (plotOrder[item] == "LABELLED"){
if(is.na(followCarbon)) followCarbon <- 2
if (followCarbon == 2){
fcMtx <-PeakML.Isotope.getFCMtxAbun(trendList, sampleGroups, followCarbon, element)
#fcMtx <-PeakML.Isotope.getFCMtxAbun(trendList, sg, followCarbon, element)
} else {
fcMtx <- PeakML.Isotope.getFCMtx(trendList, sampleGroups, followCarbon)
#fcMtx <- PeakML.Isotope.getFCMtx(trendList, sg, followCarbon)
}
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(fcMtx))
fcMtx <-subset(fcMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
if (useArea == FALSE){
# ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "mean peak height"
} else {
# ylabel <- paste(metName[1], "(mean peak area)", sep= " ")
ylabel <- "mean peak area"
}
ylimit <- max(apply(fcMtx, 2, sum)) * axExFact
if (!ylimit==0){
# par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
if (followCarbon==2){
overlap <- "#993399" # expected NA / NA whichever is smaller
expectedLarger <- "#FF9988" # expected natuabun is greater
measuredLarger <- "#8877FF" # blue
colvector <- c(overlap, expectedLarger, measuredLarger)
} else {
colvector <- fillColor[followCarbon]
}
# barplot(fcMtx, beside=FALSE, col=colvector, axisnames=FALSE, ylab=ylabel, ylim=c(0,ylimit), border=NA)
# axis(1, las=3, at=c(1:length(sampleGroups)), labels=sampleGroups, lwd=0, cex.axis=.8)
mp<-barplot(fcMtx, beside=FALSE, col=colvector, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = colnames(fcMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
# axis(1, at = mp, labels = FALSE)
title(paste("Trend of ", followCarbon-1,"", element, " labelled isotopomer"), cex.main=0.8)
#title(paste("Trend of natural abundance (", element, ")"), cex.main=0.8)
axis(2)
if (followCarbon==2){
legend("topright",fill=colvector, c("Overlap", "<Expected", ">Expected"), bty="n")
}
} else {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(0.5,0.5,0.5,0.5))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
}
} else if (plotOrder[item] == "RATIO") {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
mp<-barplot(t(ratioMtx), beside=FALSE, col=fillColor, ylab="% area under peak", ylim = c(0,1), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels = row.names(ratioMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.2)
# axis(1, at = mp, labels = FALSE)
title("Ratio", cex.main=0.8)
axis(2)
} else if (plotOrder[item] == "TOTRATIO") {
getRelAbunMtx <- function (trendList, sampleGroups, followCarbon){
numCarbons <- length(trendList[[1]])
plotMtx <- matrix(nrow = 1, ncol = length(sampleGroups))
dimnames(plotMtx) <- list(c("RelAbun"), sampleGroups)
for (sam in 1:length(sampleGroups)){
for (row in 1:length(rownames(plotMtx))){
x <- trendList[[sam]][[followCarbon]]
y <- sum(unlist(trendList[[sam]]))
if (is.null(x)){
x <- 0
}
if (is.null(y)){
y <- 0
}
plotMtx[row, sam] <- x/y*100
}
}
plotMtx
}
if(is.na(followCarbon)) followCarbon <- 2
ftMtx <- getRelAbunMtx(trendList, sampleGroups, followCarbon)
ftMtx[is.nan(ftMtx)] <- 0
if(!is.null(exclude_from_plots)){
exIndex <- match(exclude_from_plots, colnames(ftMtx))
ftMtx <-subset(ftMtx,select=-exIndex)
lbls <- setdiff(sampleGroups, sampleGroups[exclude_from_plots])
}
if (useArea == FALSE){
# ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
ylabel <- "% relative labelling"
} else {
ylabel <- "% relative labelling"
#ylabel <- paste(metName[1], "(mean peak height)", sep= " ")
}
ylimit <- max(apply(ftMtx, 2, sum)) * axExFact
if (ylimit>100) ylimit <- 100
# if (is.nan(ylimit)){ylimit<-0}
if (!ylimit==0){
# par (mar=c(2,4,2,0))
par (mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(4,2.5,0.5,3))
colvector <- fillColor[followCarbon]
mp<-barplot(ftMtx, beside=FALSE, col=colvector, ylab=ylabel, ylim=c(0,ylimit), border=NA, axisnames=FALSE, axes=FALSE)
text(mp, par("usr")[3], labels=colnames(ftMtx), srt = 45, adj = 1, xpd =TRUE, cex=0.6)
# axis(1, at = mp, labels = FALSE)
title("Relative labelling pattern", cex.main=0.8)
axis(2)
} else {
# par (mar=c(2,4,2,0))
par(mar=c(2,4,2,0), mgp=c(2,1,0))
# par(mar=c(0.5,0.5,0.5,0.5))
plot (1, 1, xlab="", ylab="", pch="", axes=F)
}
} else if (plotOrder[item] == "EMPTY"){
# This is a an empty plot for flexibility e.g. define empty if a plot is not needed
plot (1, 1, xlab="", ylab="", pch="", axes=F)
} else{
if (! length(unlist(rtList[[peakGroup]][[item]])) == 0){
maxRT <- max(unlist(rtList[[peakGroup]][[item]]),na.rm=TRUE)
minRT <- min(unlist(rtList[[peakGroup]][[item]]),na.rm=TRUE)
maxIN <- max(unlist(intList[[peakGroup]][[item]]),na.rm=TRUE)
minIN <- 0
}else{
maxRT <- 0
minRT <- 0
maxIN <- 0
minIN <- 0
}
# par(mar=c(4,4,0.5,0.5), mgp=c(1.5,0.5,0))
par(mar=c(2,2,1,0), mgp=c(0.5,0.5,0))
plot (1, 1, pch="", xlab="", ylab="", xlim=c(minRT,maxRT), ylim=c(minIN,maxIN), cex.axis=0.75)
for (isotop in 1:numCarbons){
numReplicates <- length(rtList[[peakGroup]][[item]][[isotop]])
for (rep in 1:numReplicates){
points(rtList[[peakGroup]][[item]][[isotop]][[rep]], intList[[peakGroup]][[item]][[isotop]][[rep]], type="l",col=fillColor[[isotop]])
}
}
legend("topright", plotOrder[item], bty="n", cex=.5)
}
}
}
}
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