From 89d3ead7269cd96c66bccd6e75f5b0082be121e2 Mon Sep 17 00:00:00 2001 From: Christian Panse Date: Thu, 22 Oct 2020 15:34:29 +0200 Subject: [PATCH] cosmetics #1 --- vignettes/JPR_TechnicalNote.Rmd | 14 ++++++++------ 1 file changed, 8 insertions(+), 6 deletions(-) diff --git a/vignettes/JPR_TechnicalNote.Rmd b/vignettes/JPR_TechnicalNote.Rmd index bea98d9..5c2467c 100644 --- a/vignettes/JPR_TechnicalNote.Rmd +++ b/vignettes/JPR_TechnicalNote.Rmd @@ -76,12 +76,12 @@ The binary example file sample.raw contains 574 fourier-transformed orbi trap sp ### Use Case I - Analyzing orbi trap spectra plotting using biognosys iRT peptides [@Escher2012] -```{r plot.rawRspectrum, fig.cap="plot a mass spectrum.", error=TRUE} +```{r plot.rawRspectrum, fig.cap="graphs a tandem mass spectrum of the LGGNEQVTR peptide.", error=TRUE} # http://fgcz-ms.uzh.ch/~cpanse/20181113_010_autoQC01.raw # MD5 (20181113_010_autoQC01.raw) = a1f5df9627cf9e0d51ec1906776957ab rawfile <- file.path(Sys.getenv('HOME'), @@ -100,7 +100,7 @@ and [@Gehrig2020]. ### Use Case II - Working with chromatograms - iRT regression -```{r plot.rawRchromatogram, fig.cap="plot a chromatogram (XIC)", error=TRUE} +```{r plot.rawRchromatogram, fig.cap="plots chromatograms (XIC) for a list of given target mass ranges. ", error=TRUE} iRT <- c(487.2571, 547.2984, 622.8539, 636.8695, 644.8230, 669.8384, 683.8282, 683.8541, 699.3388, 726.8361, 776.9301) @@ -109,7 +109,7 @@ names(iRT) <- c("LGGNEQVTR", "YILAGVENSK", "GTFIIDPGGVIR", "GTFIIDPAAVIR", "TPVITGAPYEYR", "DGLDAASYYAPVR", "ADVTPADFSEWSK", "LFLQFGAQGSPFLK") -C <- readChromatogram(rawfile, iRT) +C <- readChromatogram(rawfile, iRT, tol=10) plot(C) ``` @@ -121,8 +121,10 @@ rt <- sapply(C, function(x) x$times.max) fit <- lm(rt ~ score ) ``` -```{r iRTscoreFitPlot, echo=FALSE, error=TRUE} -plot(rt ~ score, pch=16,frame.plot = FALSE,asp=1); abline(fit, col='grey') +```{r iRTscoreFitPlot, echo=FALSE, error=TRUE, fig.cap="graphs the retention time verus the retention time scores."} +plot(rt ~ score, + ylab='retention time [in min]', + pch=16,frame.plot = FALSE,asp=1); abline(fit, col='grey') text(score, rt, substr(names(iRT),1,3),pos=3) text(score, rt, iRT,pos=1,cex=0.5) ```