Nothing
R/plotBatmanFit.R
In batman: Bayesian AuTomated Metabolite Analyser for NMR spectra
Defines functions
plotBatmanFit
Documented in
plotBatmanFit
plotBatmanFit<-function(BM, xfrom, xto, yfrom, yto, listMeta = FALSE, metaName, saveFig = TRUE,
saveFigDir = BM$outputDir, prefixFig, rerun = FALSE, placeLegend = "topright",
plotColour, overwriteFig = FALSE, showPlot)
{
## written by Dr. Jie Hao, Imperial College London
## plot batman metabolites fittings of NMR spectra (with down sampling)
if (missing(BM))
return(cat("Please input batman data list.\n"))
warnDef<-options("warn")$warn
warnRead<-options(warn = -1)
## os information
os <- NULL
if (missing(showPlot))
{
sysinf <- Sys.info()
os <- "notlisted"
if (!is.null(sysinf)){
os1 <- sysinf['sysname']
if (os1 == 'Darwin')
{os <- "osx"}
else if (grepl("windows", tolower(os1)))
{os<- "win"}
else if (grepl("linux", tolower(os1)))
{os<- "linux" }
} else { ## mystery machine
#os <- .Platform$OS.type
if (grepl("^darwin", R.version$os))
os <- "osx"
if (grepl("linux-gnu", R.version$os))
os <- "linux"
}
}
if (!is.null(os))
{
if (os == 'win' || os == 'osx')
{ showPlot <- TRUE }
else
{ #if (os == 'linux')
showPlot <- FALSE
cat("\nThis operating system may not support X11, no plot will be displayed, figures in .pdf format will be saved in output folder.")
cat("\nCheck input argument 'showPlot' for more detail.")
}
}
pdfdev = FALSE
ptype = "pdf"
cex = 0.8
cex1 = 0.5
ns<-5
## if missing from and to parameters, use whole spectrum
if (missing(xfrom))
xfrom = min(BM$sFit[1,1],BM$sFit[nrow(BM$sFit),1])
if (missing(xto))
xto = max(BM$sFit[1,1],BM$sFit[nrow(BM$sFit),1])
if (xfrom > xto)
{
temp<-xfrom
xfrom<-xto
xto<-temp
}
ytoIP <- 1
if (missing(yfrom))
yfrom <- 0
if (missing(yto))
{
ytoIP<-NULL
}
pind<-which(BM$sFit[,1]<=xto & BM$sFit[,1]>=xfrom)
if (length(pind)== 0)
pind<-which(BM$sFit[,1]<=xfrom & BM$sFit[,1]>=xto)
if (missing(plotColour))
{
pc1 <- rainbow(max(nrow(BM$beta)+3, 20))
pc2 <- rainbow(3)
plotColour<- sample(setdiff(pc1, pc2),nrow(BM$beta))
}
## match metabolite
nometa<-FALSE
m<-row.names(BM$beta)
if (!missing(metaName))
{
mind<-which(tolower(m) %in% (tolower(metaName)))
if (length(mind)==0) {cat("No matching metabolite found...\n")}
} else if (missing(metaName) && listMeta) {
mind<-1:length(m)
nometa<-TRUE
metaName<-"all"
} else {
mind<-NULL
nometa<-TRUE
metaName<-NULL
}
if (length(plotColour) >= length(mind))
plotColour<-plotColour[mind]
else
stop("plotColour length smaller than metabolite names.\n")
sno<-BM$specRange
n <- 2
metaTmplty <-ns
metaTmplwd <-2
outpdf1<-NULL
gind<-NULL
gapsize<-NULL
gap<-NULL
## set gap for plot
if (!is.null(BM$sFit))
{
x<-BM$sFit[pind,1]
df<-abs(diff(BM$sFit[pind,1]))
gind<-which(df>(min(df)*3))
for (gi in 1:length(gind))
gap<-rbind(gap, BM$sFit[pind[gind[gi]],1],BM$sFit[pind[gind[gi]+1],1])
gap<-(sort(gap))
lgap <- length(gap)
gapsize<-abs(diff(gap))
if (lgap>0)
gapsizeodd<-gapsize[seq(1,length(gapsize),2)]
xlim <- c(min(BM$sFit[pind,1]), max(BM$sFit[pind,1]) - gapsize[1])
xtics <- pretty(BM$sFit[pind,1],n=(abs(diff(range(x)))%/%0.05))
xticlab <- xtics
lgap <- length(gap)
lgo<-(lgap-2)/2
if (lgap>0)
{
littleones <- which(x <= gap[1])
if (lgap > 3)
{
middleones <-NULL
for (ig in 1:lgo)
{
if (ig == 1)
middleones <- list(which(x >= gap[ig*2] & x <= gap[ig*2+1]))
else
middleones[[ig]]<-which(x >= gap[ig*2] & x <= gap[ig*2+1])
}
bigones <- which(x >= gap[lgap] )
#lostones <- sum(c(x > gap[1] & x < gap[2],x > gap[3] & x < gap[4] ))
} else {
middleones <- NULL
bigones <- which(x >= gap[2])
#lostones <- sum(x > gap[1] & x < gap[2])
}
littletics <- which(xtics < gap[1])
if (length(gapsize) > 2)
{
middletics<-NULL
maxdif<-0
midshowat<-NULL
midshowlab<-NULL
middif<-NULL
for (ig in 1:lgo)
{
maxdif <- maxdif + gapsizeodd[ig]
middif<-rbind(middif, maxdif)
middletics <- which(xtics >= gap[ig*2] & xtics <=gap[ig*2+1])
midshowat<-c(midshowat, xtics[middletics] - maxdif)
midshowlab<-c(midshowlab,xticlab[middletics])
}
maxdif<-maxdif + gapsizeodd[length(gapsizeodd)]
xlim <- c(min(x), max(x)-maxdif)
bigtics <- which(xtics >= gap[lgap])
show.at <- c(xtics[littletics], midshowat, xtics[bigtics] - maxdif)
#show.at <- c(xtics[littletics], xtics[middletics] - gapsize[1], xtics[bigtics] - (gapsize[1] + gapsize[3]))
show.labels <- c(xticlab[littletics], midshowlab,xticlab[bigtics])
} else {
xlim <- c(min(x), max(x) - gapsize[1])
bigtics <- which(xtics >= gap[2])
show.at <- c(xtics[littletics], xtics[bigtics] - gapsize[1])
show.labels <- c(xticlab[littletics], xticlab[bigtics])
}
}
}
## plot batman results
if (!is.null(BM$sFit) && !rerun)
{
for (j in 1:length(sno))
{
if ((j%%n) == 1)
{
if ((length(sno)-j)>=1)
{
if (!missing(prefixFig))
outpdf1 <- paste(saveFigDir, "/", prefixFig,"_specFit_", sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
else
outpdf1 <- paste(saveFigDir,"/specFit_",sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf1))))
{
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file \"", outpdf1, "\" already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if(showPlot)
x11(20,15)
par(mfrow=c(n,1))
} else {
if (!missing(prefixFig))
outpdf1 <- paste(saveFigDir, "/", prefixFig, "_specFit_", sno[j], "_",metaName,".",ptype, sep="")
else
outpdf1 <- paste(saveFigDir,"/specFit_",sno[j],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf1))))
{
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf1, "already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else
x11(20,15)
}
}
i <- (ns*(j-1)+1)
if (is.null(ytoIP))
yto <- max(max(BM$sFit[pind,(i+1):(i+ns-1)]))
if (yfrom > yto)
{
temp<-yfrom
yfrom<-yto
yto<-temp
}
if (length(gap)>0)
{
## plot metabolites fit with gap
ylim <- c(yfrom, yto)
ytics <- pretty(ylim)
yticlab <- ytics
plot(BM$sFit[pind[littleones],i], BM$sFit[pind[littleones],i+1], xlim = rev(xlim),
ylim = ylim, axes = FALSE, lwd = 0.5, col = 4, lty = 1,
type="l", xlab="ppm", ylab="Standardized Intensity",
main=paste("NMR Spectrum ",sno[j],": ",BM$specTitle[2,j],sep=""))
box()
axis(2, at = ytics, labels = yticlab)
axis(1, at = show.at, labels = show.labels)
axis.break(1, gap[1], style = "zigzag")
if (length(gapsize) > 2) {
for (ig in 1:lgo)
{
axis.break(1, gap[ig*2+1] - middif[ig], style = "zigzag")
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+4],col=1,lwd=0.5,lty=1)
}
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
{
ytmp <- BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
} else {
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
{
ytmp <- BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
} else {
## plot metabolites fit without gap
plot(BM$sFit[pind,i],BM$sFit[pind,i+1],type="l",xlim=rev(range(BM$sFit[pind,i])),xlab="ppm",
ylab="Standardized Intensity", main=paste("NMR Spectrum ",sno[j],": ",BM$specTitle[2,j],sep=""),
ylim = c(yfrom, yto), lwd = 0.5, col = 4, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+2],col=3, lwd = 0.5, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+3],col=2, lwd = 0.5, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+4],col=1, lwd = 0.5, lty = 1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
lines(BM$sFit[pind,i],BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)],col=plotColour[i2], lwd = metaTmplwd, lty = metaTmplty )
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
for (md in 1:length(mind))
{
lines(BM$sFit[pind,i],BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty )
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
if ((length(sno) == j || !(j%%n)) && saveFig) {
if (pdfdev)
{
pdfoff = dev.off()
pdfdev = FALSE
}
else if (showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf1, "already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
df = dev.copy2pdf(device=x11, file = outpdf1)
}
else
df = dev.copy2pdf(device=x11, file = outpdf1)
#(file.exists(outpdf1) && !overwriteFig)
# cat("Can't save figure, file", outpdf1, "already exists.\n")
#else
# df = dev.copy2pdf(device=x11, file = outpdf1)
}
}
}
## plot batman rerun results
else if (!is.null(BM$sFitRerun) && rerun)
{
outpdf2 <-NULL
for (j in 1:length(sno))
{
## set subplot
if ((j%%n)==1)
{
if ((length(sno)-j)>=1)
{
if (!missing(prefixFig))
outpdf2 <- paste(saveFigDir, "/", prefixFig,"_specfitRerun_", sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
else
outpdf2 <- paste(saveFigDir,"/specfitRerun_",sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf2))))
{
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
pdf(outpdf2,20, 15)
pdfdev = TRUE
}
else
x11(20,15)
par(mfrow=c(n,1))
} else {
if (!missing(prefixFig))
outpdf2 <- paste(saveFigDir, "/", prefixFig,"_specfitRerun_", sno[j], "_",metaName,".",ptype, sep="")
else
outpdf2 <- paste(saveFigDir,"/specfitRerun_",sno[j],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf2))))
{
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else
x11(20,15)
}
}
i = ns*(j-1)+1
if (is.null(ytoIP))
yto <- max(max(BM$sFitRerun[pind,i+1]),max(BM$sFitRerun[pind,i+2]),max(BM$sFitRerun[pind,i+3]),max(BM$sFitRerun[pind,i+4]))
if (yfrom > yto)
{
temp<-yfrom
yfrom<-yto
yto<-temp
}
if (length(gap)>0)
{
## plot metabolites fit with gap
ylim <- c(yfrom, yto)
ytics <- pretty(ylim)
yticlab <- ytics
plot(BM$sFitRerun[pind[littleones],i], BM$sFitRerun[pind[littleones],i+1], xlim = rev(xlim),
ylim = ylim, axes = FALSE, lwd = 0.5, col = 4, lty = 1,type="l", xlab="ppm", ylab="Standardized Intensity",
main=paste("NMR Spectrum ",sno[j], ": ",BM$specTitle[2,j],"(Rerun)", sep=""))
box()
axis(2, at = ytics, labels = yticlab)
axis(1, at = show.at, labels = show.labels)
axis.break(1, gap[1], style = "zigzag")
if (length(gapsize) > 2) {
for (ig in 1:lgo)
{
axis.break(1, gap[ig*2+1] - middif[ig], style = "zigzag")
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+4],col=1,lwd=0.5,lty=1)
}
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
{
ytmp <- BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
} else {
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
{
ytmp <- BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
} else {
## plot metabolites fit without gap
plot(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+1],type="l",xlim=rev(range(BM$sFitRerun[pind,i])),xlab="ppm",
ylab="Standardized Intensity", main=paste("NMR Spectrum ",sno[j], ": ",BM$specTitle[2,j],"(Rerun)", sep=""),
ylim = c(yfrom, yto), lwd = 0.5, col = 4, lty = 1)
#axis(1, 1:length(pind), lab = format(BM$sFitRerun[pind,i]),xlim=rev(range(BM$sFitRerun[pind,i])))
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+2],col=3, lwd = 0.5, lty = 1)
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+3],col=2, lwd = 0.5, lty = 1)
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+4],col=1, lwd = 0.5, lty = 1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
lines(BM$sFitRerun[pind,i],BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)],col=plotColour[i2], lwd = metaTmplwd, lty = metaTmplty )
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5, 0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
for (md in 1:length(mind))
{
lines(BM$sFitRerun[pind,i],BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty )
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
## save plot
if ((length(sno) == j || !(j%%n)) && saveFig)
{
if (pdfdev)
{
pdfoff = dev.off()
pdfdev = FALSE
}
else if (showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
df = dev.copy2pdf(device=x11, file = outpdf2)
}
else
df = dev.copy2pdf(device=x11, file = outpdf2)
## if (file.exists(outpdf2) && !(overwriteFig))
## cat("Can't save figure, file", outpdf2, "already exists.\n")
## else
## df = dev.copy2pdf(device=x11, file = outpdf2)
}
}
} else {
cat("No results found.\n")
}
warnRead<-options(warn = warnDef)
}
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R Package Documentation
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Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions plotBatmanFit
Documented in plotBatmanFit
plotBatmanFit<-function(BM, xfrom, xto, yfrom, yto, listMeta = FALSE, metaName, saveFig = TRUE,
saveFigDir = BM$outputDir, prefixFig, rerun = FALSE, placeLegend = "topright",
plotColour, overwriteFig = FALSE, showPlot)
{
## written by Dr. Jie Hao, Imperial College London
## plot batman metabolites fittings of NMR spectra (with down sampling)
if (missing(BM))
return(cat("Please input batman data list.\n"))
warnDef<-options("warn")$warn
warnRead<-options(warn = -1)
## os information
os <- NULL
if (missing(showPlot))
{
sysinf <- Sys.info()
os <- "notlisted"
if (!is.null(sysinf)){
os1 <- sysinf['sysname']
if (os1 == 'Darwin')
{os <- "osx"}
else if (grepl("windows", tolower(os1)))
{os<- "win"}
else if (grepl("linux", tolower(os1)))
{os<- "linux" }
} else { ## mystery machine
#os <- .Platform$OS.type
if (grepl("^darwin", R.version$os))
os <- "osx"
if (grepl("linux-gnu", R.version$os))
os <- "linux"
}
}
if (!is.null(os))
{
if (os == 'win' || os == 'osx')
{ showPlot <- TRUE }
else
{ #if (os == 'linux')
showPlot <- FALSE
cat("\nThis operating system may not support X11, no plot will be displayed, figures in .pdf format will be saved in output folder.")
cat("\nCheck input argument 'showPlot' for more detail.")
}
}
pdfdev = FALSE
ptype = "pdf"
cex = 0.8
cex1 = 0.5
ns<-5
## if missing from and to parameters, use whole spectrum
if (missing(xfrom))
xfrom = min(BM$sFit[1,1],BM$sFit[nrow(BM$sFit),1])
if (missing(xto))
xto = max(BM$sFit[1,1],BM$sFit[nrow(BM$sFit),1])
if (xfrom > xto)
{
temp<-xfrom
xfrom<-xto
xto<-temp
}
ytoIP <- 1
if (missing(yfrom))
yfrom <- 0
if (missing(yto))
{
ytoIP<-NULL
}
pind<-which(BM$sFit[,1]<=xto & BM$sFit[,1]>=xfrom)
if (length(pind)== 0)
pind<-which(BM$sFit[,1]<=xfrom & BM$sFit[,1]>=xto)
if (missing(plotColour))
{
pc1 <- rainbow(max(nrow(BM$beta)+3, 20))
pc2 <- rainbow(3)
plotColour<- sample(setdiff(pc1, pc2),nrow(BM$beta))
}
## match metabolite
nometa<-FALSE
m<-row.names(BM$beta)
if (!missing(metaName))
{
mind<-which(tolower(m) %in% (tolower(metaName)))
if (length(mind)==0) {cat("No matching metabolite found...\n")}
} else if (missing(metaName) && listMeta) {
mind<-1:length(m)
nometa<-TRUE
metaName<-"all"
} else {
mind<-NULL
nometa<-TRUE
metaName<-NULL
}
if (length(plotColour) >= length(mind))
plotColour<-plotColour[mind]
else
stop("plotColour length smaller than metabolite names.\n")
sno<-BM$specRange
n <- 2
metaTmplty <-ns
metaTmplwd <-2
outpdf1<-NULL
gind<-NULL
gapsize<-NULL
gap<-NULL
## set gap for plot
if (!is.null(BM$sFit))
{
x<-BM$sFit[pind,1]
df<-abs(diff(BM$sFit[pind,1]))
gind<-which(df>(min(df)*3))
for (gi in 1:length(gind))
gap<-rbind(gap, BM$sFit[pind[gind[gi]],1],BM$sFit[pind[gind[gi]+1],1])
gap<-(sort(gap))
lgap <- length(gap)
gapsize<-abs(diff(gap))
if (lgap>0)
gapsizeodd<-gapsize[seq(1,length(gapsize),2)]
xlim <- c(min(BM$sFit[pind,1]), max(BM$sFit[pind,1]) - gapsize[1])
xtics <- pretty(BM$sFit[pind,1],n=(abs(diff(range(x)))%/%0.05))
xticlab <- xtics
lgap <- length(gap)
lgo<-(lgap-2)/2
if (lgap>0)
{
littleones <- which(x <= gap[1])
if (lgap > 3)
{
middleones <-NULL
for (ig in 1:lgo)
{
if (ig == 1)
middleones <- list(which(x >= gap[ig*2] & x <= gap[ig*2+1]))
else
middleones[[ig]]<-which(x >= gap[ig*2] & x <= gap[ig*2+1])
}
bigones <- which(x >= gap[lgap] )
#lostones <- sum(c(x > gap[1] & x < gap[2],x > gap[3] & x < gap[4] ))
} else {
middleones <- NULL
bigones <- which(x >= gap[2])
#lostones <- sum(x > gap[1] & x < gap[2])
}
littletics <- which(xtics < gap[1])
if (length(gapsize) > 2)
{
middletics<-NULL
maxdif<-0
midshowat<-NULL
midshowlab<-NULL
middif<-NULL
for (ig in 1:lgo)
{
maxdif <- maxdif + gapsizeodd[ig]
middif<-rbind(middif, maxdif)
middletics <- which(xtics >= gap[ig*2] & xtics <=gap[ig*2+1])
midshowat<-c(midshowat, xtics[middletics] - maxdif)
midshowlab<-c(midshowlab,xticlab[middletics])
}
maxdif<-maxdif + gapsizeodd[length(gapsizeodd)]
xlim <- c(min(x), max(x)-maxdif)
bigtics <- which(xtics >= gap[lgap])
show.at <- c(xtics[littletics], midshowat, xtics[bigtics] - maxdif)
#show.at <- c(xtics[littletics], xtics[middletics] - gapsize[1], xtics[bigtics] - (gapsize[1] + gapsize[3]))
show.labels <- c(xticlab[littletics], midshowlab,xticlab[bigtics])
} else {
xlim <- c(min(x), max(x) - gapsize[1])
bigtics <- which(xtics >= gap[2])
show.at <- c(xtics[littletics], xtics[bigtics] - gapsize[1])
show.labels <- c(xticlab[littletics], xticlab[bigtics])
}
}
}
## plot batman results
if (!is.null(BM$sFit) && !rerun)
{
for (j in 1:length(sno))
{
if ((j%%n) == 1)
{
if ((length(sno)-j)>=1)
{
if (!missing(prefixFig))
outpdf1 <- paste(saveFigDir, "/", prefixFig,"_specFit_", sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
else
outpdf1 <- paste(saveFigDir,"/specFit_",sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf1))))
{
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file \"", outpdf1, "\" already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if(showPlot)
x11(20,15)
par(mfrow=c(n,1))
} else {
if (!missing(prefixFig))
outpdf1 <- paste(saveFigDir, "/", prefixFig, "_specFit_", sno[j], "_",metaName,".",ptype, sep="")
else
outpdf1 <- paste(saveFigDir,"/specFit_",sno[j],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf1))))
{
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf1, "already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
pdf(outpdf1,20,15)
pdfdev = TRUE
}
else
x11(20,15)
}
}
i <- (ns*(j-1)+1)
if (is.null(ytoIP))
yto <- max(max(BM$sFit[pind,(i+1):(i+ns-1)]))
if (yfrom > yto)
{
temp<-yfrom
yfrom<-yto
yto<-temp
}
if (length(gap)>0)
{
## plot metabolites fit with gap
ylim <- c(yfrom, yto)
ytics <- pretty(ylim)
yticlab <- ytics
plot(BM$sFit[pind[littleones],i], BM$sFit[pind[littleones],i+1], xlim = rev(xlim),
ylim = ylim, axes = FALSE, lwd = 0.5, col = 4, lty = 1,
type="l", xlab="ppm", ylab="Standardized Intensity",
main=paste("NMR Spectrum ",sno[j],": ",BM$specTitle[2,j],sep=""))
box()
axis(2, at = ytics, labels = yticlab)
axis(1, at = show.at, labels = show.labels)
axis.break(1, gap[1], style = "zigzag")
if (length(gapsize) > 2) {
for (ig in 1:lgo)
{
axis.break(1, gap[ig*2+1] - middif[ig], style = "zigzag")
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],BM$sFit[pind[middleones[[ig]]],i+4],col=1,lwd=0.5,lty=1)
}
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-maxdif,BM$sFit[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
{
ytmp <- BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFit[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
} else {
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFit[pind[littleones],i],BM$sFit[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),BM$sFit[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
{
ytmp <- BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)]
lines(BM$sFit[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFit[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
} else {
## plot metabolites fit without gap
plot(BM$sFit[pind,i],BM$sFit[pind,i+1],type="l",xlim=rev(range(BM$sFit[pind,i])),xlab="ppm",
ylab="Standardized Intensity", main=paste("NMR Spectrum ",sno[j],": ",BM$specTitle[2,j],sep=""),
ylim = c(yfrom, yto), lwd = 0.5, col = 4, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+2],col=3, lwd = 0.5, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+3],col=2, lwd = 0.5, lty = 1)
lines(BM$sFit[pind,i],BM$sFit[pind,i+4],col=1, lwd = 0.5, lty = 1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$beta))
lines(BM$sFit[pind,i],BM$beta[i2,j]*BM$metaTemp[pind,i2+(j-1)*nrow(BM$beta)],col=plotColour[i2], lwd = metaTmplwd, lty = metaTmplty )
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$beta))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$beta))))
} else if (length(mind)!=0) {
## plot named metabolite
for (md in 1:length(mind))
{
lines(BM$sFit[pind,i],BM$beta[mind[md],j]*BM$metaTemp[pind,mind[md]+(j-1)*nrow(BM$beta)],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty )
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$beta)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
if ((length(sno) == j || !(j%%n)) && saveFig) {
if (pdfdev)
{
pdfoff = dev.off()
pdfdev = FALSE
}
else if (showPlot && (file.exists(outpdf1) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf1, "already exists.\n")
tmpOP <- strsplit(outpdf1, "[.]")
outpdf1 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf1, "\".\n")
df = dev.copy2pdf(device=x11, file = outpdf1)
}
else
df = dev.copy2pdf(device=x11, file = outpdf1)
#(file.exists(outpdf1) && !overwriteFig)
# cat("Can't save figure, file", outpdf1, "already exists.\n")
#else
# df = dev.copy2pdf(device=x11, file = outpdf1)
}
}
}
## plot batman rerun results
else if (!is.null(BM$sFitRerun) && rerun)
{
outpdf2 <-NULL
for (j in 1:length(sno))
{
## set subplot
if ((j%%n)==1)
{
if ((length(sno)-j)>=1)
{
if (!missing(prefixFig))
outpdf2 <- paste(saveFigDir, "/", prefixFig,"_specfitRerun_", sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
else
outpdf2 <- paste(saveFigDir,"/specfitRerun_",sno[j], "to",sno[j+n-1],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf2))))
{
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
pdf(outpdf2,20, 15)
pdfdev = TRUE
}
else
x11(20,15)
par(mfrow=c(n,1))
} else {
if (!missing(prefixFig))
outpdf2 <- paste(saveFigDir, "/", prefixFig,"_specfitRerun_", sno[j], "_",metaName,".",ptype, sep="")
else
outpdf2 <- paste(saveFigDir,"/specfitRerun_",sno[j],"_",metaName,".",ptype, sep="")
if ((!showPlot && overwriteFig) || (!showPlot && (!file.exists(outpdf2))))
{
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else if (!showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
pdf(outpdf2,20,15)
pdfdev = TRUE
}
else
x11(20,15)
}
}
i = ns*(j-1)+1
if (is.null(ytoIP))
yto <- max(max(BM$sFitRerun[pind,i+1]),max(BM$sFitRerun[pind,i+2]),max(BM$sFitRerun[pind,i+3]),max(BM$sFitRerun[pind,i+4]))
if (yfrom > yto)
{
temp<-yfrom
yfrom<-yto
yto<-temp
}
if (length(gap)>0)
{
## plot metabolites fit with gap
ylim <- c(yfrom, yto)
ytics <- pretty(ylim)
yticlab <- ytics
plot(BM$sFitRerun[pind[littleones],i], BM$sFitRerun[pind[littleones],i+1], xlim = rev(xlim),
ylim = ylim, axes = FALSE, lwd = 0.5, col = 4, lty = 1,type="l", xlab="ppm", ylab="Standardized Intensity",
main=paste("NMR Spectrum ",sno[j], ": ",BM$specTitle[2,j],"(Rerun)", sep=""))
box()
axis(2, at = ytics, labels = yticlab)
axis(1, at = show.at, labels = show.labels)
axis.break(1, gap[1], style = "zigzag")
if (length(gapsize) > 2) {
for (ig in 1:lgo)
{
axis.break(1, gap[ig*2+1] - middif[ig], style = "zigzag")
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],BM$sFitRerun[pind[middleones[[ig]]],i+4],col=1,lwd=0.5,lty=1)
}
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,BM$sFitRerun[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
{
ytmp <- BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
for (ig in 1:lgo)
lines(BM$sFitRerun[pind[middleones[[ig]]],i]-middif[ig],ytmp[middleones[[ig]]],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-maxdif,ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
} else {
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+1],col=4,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+2],col=3,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+3],col=2,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[littleones],i],BM$sFitRerun[pind[littleones],i+4],col=1,lwd=0.5,lty=1)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),BM$sFitRerun[pind[bigones],i+4],col=1,lwd=0.5,lty=1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
{
ytmp <- BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[i2],lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
## lines(BM$beta[mind,j]*BM$metaTemp[pind,mind+(j-1)*nrow(BM$beta)],col=plotColour[mind], lwd = metaTmplwd, lty = metaTmplty )
for (md in 1:length(mind))
{
ytmp <- BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)]
lines(BM$sFitRerun[pind[littleones],i],ytmp[littleones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
lines(BM$sFitRerun[pind[bigones],i]-(gapsize[1]),ytmp[bigones],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty)
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
} else {
## plot metabolites fit without gap
plot(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+1],type="l",xlim=rev(range(BM$sFitRerun[pind,i])),xlab="ppm",
ylab="Standardized Intensity", main=paste("NMR Spectrum ",sno[j], ": ",BM$specTitle[2,j],"(Rerun)", sep=""),
ylim = c(yfrom, yto), lwd = 0.5, col = 4, lty = 1)
#axis(1, 1:length(pind), lab = format(BM$sFitRerun[pind,i]),xlim=rev(range(BM$sFitRerun[pind,i])))
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+2],col=3, lwd = 0.5, lty = 1)
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+3],col=2, lwd = 0.5, lty = 1)
lines(BM$sFitRerun[pind,i],BM$sFitRerun[pind,i+4],col=1, lwd = 0.5, lty = 1)
if (listMeta && nometa)
{
## if listMeta is TRUE and missing metabolite name, plot all
for (i2 in 1:nrow(BM$betaRerun))
lines(BM$sFitRerun[pind,i],BM$betaRerun[i2,j]*BM$metaTempRerun[pind,i2+(j-1)*nrow(BM$betaRerun)],col=plotColour[i2], lwd = metaTmplwd, lty = metaTmplty )
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)), col=c(4,3,2,1,plotColour), ncol = 2, cex = cex1,
lty=c(1,1,1,1,rep(metaTmplty, nrow(BM$betaRerun))),lwd = c(0.5,0.5,0.5, 0.5,rep(metaTmplwd, nrow(BM$betaRerun))))
} else if (length(mind)!=0) {
## plot named metabolite
for (md in 1:length(mind))
{
lines(BM$sFitRerun[pind,i],BM$betaRerun[mind[md],j]*BM$metaTempRerun[pind,mind[md]+(j-1)*nrow(BM$betaRerun)],col=plotColour[md], lwd = metaTmplwd, lty = metaTmplty )
}
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum",
row.names(BM$betaRerun)[mind]), col=c(4,3,2,1,plotColour), cex = cex,
lty=c(1,1,1,1,rep(metaTmplty, length(mind))),lwd = c(0.5,0.5,0.5,0.5,rep(metaTmplwd, length(mind))))
} else {
legend(placeLegend, c("Original Spectrum", "Metabolites Fit", "Wavelet Fit", "Fit Sum"), col=c(4,3,2,1),
lty=c(1,1,1,1),lwd = c(0.5,0.5,0.5,0.5), cex = cex)
}
}
## save plot
if ((length(sno) == j || !(j%%n)) && saveFig)
{
if (pdfdev)
{
pdfoff = dev.off()
pdfdev = FALSE
}
else if (showPlot && (file.exists(outpdf2) && !overwriteFig))
{
cat("\nCan't save figure, file", outpdf2, "already exists.\n")
tmpOP <- strsplit(outpdf2, "[.]")
outpdf2 <- paste(tmpOP[[1]][1], "_", format(Sys.time(), "%d_%b_%H_%M_%S"), ".", tmpOP[[1]][2], sep = "")
cat("Figure saved in new file \"", outpdf2, "\".\n")
df = dev.copy2pdf(device=x11, file = outpdf2)
}
else
df = dev.copy2pdf(device=x11, file = outpdf2)
## if (file.exists(outpdf2) && !(overwriteFig))
## cat("Can't save figure, file", outpdf2, "already exists.\n")
## else
## df = dev.copy2pdf(device=x11, file = outpdf2)
}
}
} else {
cat("No results found.\n")
}
warnRead<-options(warn = warnDef)
}
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