cosmetics #1

fgcz · Oct 22, 2020 · 89d3ead · 89d3ead
1 parent eb40303
commit 89d3ead
Showing 1 changed file with 8 additions and 6 deletions.
diff --git 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
 <!---
-scp r35:/export/lv_iduzh06/projects/p1000/Proteomics/QEXACTIVEHF_2/tobiasko_20181113/20181113_010_autoQC01.raw ~/Downloads/
+scp fgcz-r-035.uzh.ch:/export/lv_iduzh06/projects/p1000/Proteomics/QEXACTIVEHF_2/tobiasko_20181113/20181113_010_autoQC01.raw ~/Downloads/
 -->
 
 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)
 ```