### R code from vignette source 'poster.Rnw' ################################################### ### code chunk number 1: style-Sweave ################################################### options(prompt = "R> ", continue = "+ ", width = 60, useFancyQuotes = FALSE) ################################################### ### code chunk number 2: digest ################################################### library(protViz) irt.peptide <- as.character( protViz::iRTpeptides$peptide) irt.pim <- parentIonMass(irt.peptide) op <- par(mfrow = c(1,2), pch = 16, col = rgb(0.5, 0.5, 0.5, alpha = 0.5)) hist(irt.pim, xlab="peptide mass [in Da]") irt.ssrc <- sapply(irt.peptide, ssrc) plot(irt.pim ~ irt.ssrc, cex = 2, main = 'In-silico LC-MS map') par(op) ################################################### ### code chunk number 3: poster.Rnw:149-152 ################################################### defaultIon peptides <- c('HTLNQIDSVK') fi <- fragmentIon(peptides) ################################################### ### code chunk number 4: insilico ################################################### par <- par(mfrow = c(1, 1)) pim <- parentIonMass(peptides) for (i in 1:length(peptides)){ plot(0,0, xlab='m/Z', ylab='', xlim=range(c(fi[i][[1]]$b,fi[i][[1]]$y)), ylim=c(0, 1), type='n', axes=FALSE, sub=paste( pim[i], "Da")); box() axis(1,fi[i][[1]]$b,round(fi[i][[1]]$b,2)) pepSeq <- strsplit(peptides[i],"") axis(3,fi[i][[1]]$b,pepSeq[[1]]) abline(v=fi[i][[1]]$b, col='red',lwd=2) abline(v=fi[i][[1]]$c, col='orange') abline(v=fi[i][[1]]$y, col='blue',lwd=2) abline(v=fi[i][[1]]$z, col='cyan') } par(op) ################################################### ### code chunk number 5: poster.Rnw:187-192 ################################################### fi.HTLNQIDSVK.1 <- fragmentIon('HTLNQIDSVK')[[1]] Hydrogen <- 1.007825 fi.HTLNQIDSVK.2 <- (fi.HTLNQIDSVK.1 + Hydrogen) / 2 ################################################### ### code chunk number 6: xtable2 ################################################### df <- as.data.frame(cbind(fi.HTLNQIDSVK.1, fi.HTLNQIDSVK.2)) names(df) <- c(paste(names(fi.HTLNQIDSVK.1),1,sep=''), paste(names(fi.HTLNQIDSVK.2),2,sep='')) library(xtable) print.xtable(xtable(df, caption = "Singly and doubly charged fragment ions of the HTLNQIDSVK tryptic peptide of the SwissProt P12763 FETUA BOVIN Alpha-2-HS-glycoprotein protein are listed.", label = "Table:xtable2"), include.rownames = FALSE, table.placement = "H", scalebox = 0.8) ################################################### ### code chunk number 7: poster.Rnw:221-236 ################################################### spec <- list(scans=1138, title = "178: (rt=22.3807) [20080816_23_fetuin_160.RAW]", rtinseconds = 1342.8402, charge = 2, mZ = c(195.139940, 221.211970, 239.251780, 290.221750, 316.300770, 333.300050, 352.258420, 448.384360, 466.348830, 496.207570, 509.565910, 538.458310, 547.253380, 556.173940, 560.358050, 569.122080, 594.435500, 689.536940, 707.624790, 803.509240, 804.528220, 822.528020, 891.631250, 909.544400, 916.631600, 973.702160, 990.594520, 999.430580, 1008.583600, 1017.692500, 1027.605900), intensity=c(931.8, 322.5, 5045, 733.9, 588.8, 9186, 604.6, 1593, 531.8, 520.4, 976.4, 410.5, 2756, 2279, 5819, 2.679e+04, 1267, 1542, 979.2, 9577, 3283, 9441, 1520, 1310, 1.8e+04, 587.5, 2685, 671.7, 3734, 8266, 3309)) ################################################### ### code chunk number 8: poster.Rnw:239-248 ################################################### peptideSequence <- 'HTLNQIDSVK' str(spec, nchar.max = 25, vec.len = 2) fi <- fragmentIon(peptideSequence) n <- nchar(peptideSequence) by.mZ <- c(fi[[1]]$b, fi[[1]]$y) idx <- findNN(by.mZ, spec$mZ) mZ.error <- abs(spec$mZ[idx]-by.mZ) which(mZ.error < 0.3) ################################################### ### code chunk number 9: peakplot ################################################### p <- peakplot('HTLNQIDSVK', spec) ################################################### ### code chunk number 10: LFQtrellis ################################################### library(lattice) data(fetuinLFQ) cv <- 1-1:7/10 t<-trellis.par.get("strip.background") t$col<-(rgb(cv,cv,cv)) trellis.par.set("strip.background",t) print(xyplot(abundance ~ conc | prot * method, groups = prot, xlab = "Fetuin concentration spiked into experiment [fmol]", ylab = "Abundance", aspect = 1, data = fetuinLFQ$t3pq[fetuinLFQ$t3pq$prot %in% c('Fetuin', 'P15891', 'P32324', 'P34730'),], panel = function(x, y, subscripts, groups) { if (groups[subscripts][1] == "Fetuin") { panel.fill(col="#ffcccc") } panel.grid(h=-1,v=-1) panel.xyplot(x, y) panel.loess(x,y, span=1) if (groups[subscripts][1] == "Fetuin") { panel.text(min(fetuinLFQ$t3pq$conc), max(fetuinLFQ$t3pq$abundance), paste("R-squared:", round(summary(lm(x~y))$r.squared,2)), cex=0.75, pos=4) } } )) ################################################### ### code chunk number 11: poster.Rnw:328-330 ################################################### data(pgLFQfeature) data(pgLFQprot) ################################################### ### code chunk number 12: featureDensityPlot ################################################### par(mfrow = c(1,1)); data(pgLFQfeature) data(pgLFQprot) protViz:::.featureDensityPlot( asinh( pgLFQfeature$"Normalized abundance"), nbins=25) ################################################### ### code chunk number 13: image1 ################################################### op <- par(mfrow=c(1,1), mar = c(18,18,4,1), cex=0.5) samples <- names(pgLFQfeature$"Normalized abundance") image(cor( asinh( pgLFQfeature$"Normalized abundance")), col = gray(seq(0,1,length=20)), asp = 1, main = 'pgLFQfeature correlation', axes=FALSE) axis(1, at=seq(from = 0, to = 1, length.out=length(samples)), labels=samples, las=2) axis(2, at=seq(from = 0, to = 1, length.out=length(samples)), labels=samples, las=2) par(op) ################################################### ### code chunk number 14: image2 ################################################### op<-par(mfrow=c(1,1),mar=c(18,18,4,1), cex=0.5) image(cor(asinh(pgLFQprot$"Normalized abundance")), main = 'pgLFQprot correlation', asp = 1, axes = FALSE, col = gray(seq(0,1,length=20))) axis(1,at=seq(from=0, to=1, length.out=length(samples)), labels=samples, las=2) axis(2,at=seq(from=0, to=1, length.out=length(samples)), labels=samples, las=2) par(op) ################################################### ### code chunk number 15: ANOVA ################################################### par(mfrow=c(1,4),mar=c(6,3,4,1)) ANOVA <- pgLFQaov( pgLFQprot$"Normalized abundance", groups=as.factor(pgLFQprot$grouping), names=pgLFQprot$output$Accession, idx=c(15,16,196,107), plot=TRUE) ################################################### ### code chunk number 16: iTRAQqqnorm ################################################### data(iTRAQ) par(mfrow = c(2,4), mar = c(6,4,3,0.5)); for (i in 3:10){ qqnorm(asinh(iTRAQ[,i]), asp = 1, main=names(iTRAQ)[i]) qqline(asinh(iTRAQ[,i]), col='grey') } ################################################### ### code chunk number 17: iTRAQboxplot ################################################### b <- boxplot(asinh(iTRAQ[, c(3:10)]), main='boxplot iTRAQ') ################################################### ### code chunk number 18: iTRAQboxplot2 ################################################### data(iTRAQ) group1Protein<-numeric() group2Protein<-numeric() for (i in c(3,4,5,6)) group1Protein<-cbind(group1Protein, asinh(tapply(iTRAQ[,i], paste(iTRAQ$prot), sum, na.rm=TRUE))) for (i in 7:10) group2Protein<-cbind(group2Protein, asinh(tapply(iTRAQ[,i], paste(iTRAQ$prot), sum, na.rm=TRUE))) par(mfrow = c(1,4), mar = c(6,3,4,1)) for (i in 1:nrow(group1Protein)){ boxplot.color="#ffcccc" tt.p_value <- t.test(as.numeric(group1Protein[i,]), as.numeric(group2Protein[i,]))$p.value if (tt.p_value < 0.05) boxplot.color='lightgreen' b <- boxplot(as.numeric(group1Protein[i,]), as.numeric(group2Protein[i,]), main=row.names(group1Protein)[i], sub=paste("t-Test: p-value =", round(tt.p_value,2)), col=boxplot.color, axes=F) axis(1, 1:2, c('group_1','group_2')); axis(2); box() points(rep(1,b$n[1]), as.numeric(group1Protein[i,]), col='blue') points(rep(2,b$n[2]), as.numeric(group2Protein[i,]), col='blue') }