fix errors

Author: lgatto

NEWS.md

@@ -1,5 +1,9 @@
 # MSnbase 2.37
 
+## 2.37.2
+- Fixing vignette (see #613)
+- use `MsDataHub` for TMT mzid data.
+
 ## 2.37.1
 - Fixing tests
 

R/plotting-Spectrum.R

@@ -34,7 +34,7 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
                                     xlim, ylim,
                                     legend.cex = 1,
                                     peaks.pch = 19, ...) {
-  if (norm) 
+  if (norm)
     spectra <- lapply(spectra, normalize)
 
   if (missing(xlim)) {
@@ -48,10 +48,10 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
     ylim <- c(-maxInten, maxInten)
   }
 
-  if (missing(common)) 
+  if (missing(common))
     common <- lapply(spectra, function(x)logical(peaksCount(x)))
 
-  if (missing(sequences)) 
+  if (missing(sequences))
     sequences <- character(2)
 
   orientation <- c(1, -1)
@@ -71,7 +71,7 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
     if (msLevel(spectra[[i]]) == 1) {
         label <- paste0("Retention time: ", formatRt(rtime(spectra[[i]])),
                         ", # common: ", sum(common[[i]]))
-        
+
     } else {
         label <- paste0("prec scan: ", precScanNum(spectra[[i]]))
         if (peaksCount(spectra[[i]])) {
@@ -124,9 +124,10 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
                                 fragments = calculateFragments_Spectrum2(object,
                                   sequence = sequence, tolerance = tolerance,
                                   relative = relative, type = type, z = z,
-                                  modifications = modifications,
+                                  fixed_modifications = modifications,
                                   neutralLoss = neutralLoss,
-                                  verbose = isMSnbaseVerbose()),
+                                  verbose = isMSnbaseVerbose()) |>
+                               suppressWarnings(),
                                fragments.cex = 0.75, peaks.lwd = 1, peaks.cex = 0.5, ...) {
   if (peaksCount(object) > 0 && !centroided(object)) {
     message("Your spectrum is not centroided.")
@@ -159,4 +160,3 @@ plotSpectrumVsSpectrum <- function(spectra, tolerance=25e-6,
          cex=fragments.cex, col="#808080")
   }
 }
-

vignettes/v01-MSnbase-demo.Rmd

@@ -37,6 +37,7 @@ suppressPackageStartupMessages(require("Rdisop"))
 suppressPackageStartupMessages(require("pRolocdata"))
 suppressPackageStartupMessages(require("pRoloc"))
 suppressPackageStartupMessages(require("msdata"))
+suppressPackageStartupMessages(require("MsDataHub"))
 library("grid")
 suppressPackageStartupMessages(library("BiocParallel"))
 ```
@@ -140,7 +141,7 @@ more details). To make use of the new *on-disk* implementation, set
 ```{r readdata, echo=TRUE, cache=FALSE, tidy=FALSE}
 file <- dir(system.file(package = "MSnbase", dir = "extdata"),
             full.names = TRUE, pattern = "mzXML$")
-rawdata <- readMSData(file, msLevel = 2, verbose = FALSE)
+rawdata <- readMSData(file, msLevel. = 2, verbose = FALSE)
 ```
 
 Only spectra of a given MS level can be loaded at a time by setting
@@ -514,9 +515,8 @@ interface by converting the dedicated identification data objects into
 `data.frames`.
 
 ```{r iddf0}
-library("msdata")
-f <- "TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01-20141210.mzid"
-idf <- msdata::ident(full.names = TRUE, pattern = f)
+library("MsDataHub")
+idf <- MsDataHub::TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.20141210.mzid()
 iddf <- readMzIdData(idf)
 str(iddf)
 ```
@@ -608,10 +608,10 @@ details.
 ```{r msnexpIdentification, echo=TRUE, cache=FALSE, tidy=FALSE}
 ## find path to a mzXML file
 quantFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
-                 full.name = TRUE, pattern = "mzXML$")
+                 full.names = TRUE, pattern = "mzXML$")
 ## find path to a mzIdentML file
 identFile <- dir(system.file(package = "MSnbase", dir = "extdata"),
-                 full.name = TRUE, pattern = "dummyiTRAQ.mzid")
+                 full.names = TRUE, pattern = "dummyiTRAQ.mzid")
 ## create basic MSnExp
 msexp <- readMSData(quantFile, verbose = FALSE)
 head(fData(msexp), n = 2)