fix 11 using Under development (unstable) (2020-02-29 r77878)

cpanse · Mar 1, 2020 · 1eb514f · 1eb514f
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,13 +1,13 @@
 Package: protViz
 Type: Package
 Title: Visualizing and Analyzing Mass Spectrometry Related Data in Proteomics
-Version: 0.6.1
+Version: 0.6.2
 Authors@R: c(person("Christian", "Panse", email = "cp@fgcz.ethz.ch", role = c("aut", "cre"), 
         comment = c(ORCID = "0000-0003-1975-3064")),
 	person("Jonas", "Grossmann", email = "jg@fgcz.ethz.ch", role = "aut",
 	comment = c(ORCID = "0000-0002-6899-9020")),
 	person("Simon", "Barkow-Oesterreicher", role = "ctb"))
-Depends: R (>= 3.5),
+Depends: R (>= 3.6),
 	methods
 Imports: Rcpp (>= 1.0)
 LinkingTo: Rcpp (>= 1.0)

diff --git a/R/PTM_MarkerFinder.R b/R/PTM_MarkerFinder.R
@@ -204,7 +204,7 @@ PTM_MarkerFinder <- function(data,
                     modified=substr(data[[i]]$modification, 2, nchar(data[[i]]$modification)-1),
                     modification=modification)
 
-                fi.by<-as.data.frame(cbind(b=fi[[1]]$b, y=fi[[1]]$y))
+                fi.by<-as.data.frame(cbind(b=fi[[1]]$b, y=fi[[1]]$y), stringsAsFactors = TRUE)
 
                 peakplot(data[[i]]$peptideSequence, 
                     spec=data[[i]], fi=fi.by, ion.axes=FALSE,  
@@ -253,14 +253,14 @@ PTM_MarkerFinder <- function(data,
                 .PTM_MarkerFinder_writeMGF(data[[k]], mgfFilename)
            }
 
-            fi<-fragmentIon(sequence=data[[k]]$peptideSequence, 
+            fi <- fragmentIon(sequence=data[[k]]$peptideSequence, 
                 FUN=defaultIon,
                 modified=substr(data[[k]]$modification, 2, nchar(data[[k]]$modification)-1),
                 modification=modification)
 
-            fi.cyz<-as.data.frame(cbind(y=fi[[1]]$y, c=fi[[1]]$c, z=fi[[1]]$z))
+            fi.cyz <- as.data.frame(cbind(y=fi[[1]]$y, c=fi[[1]]$c, z=fi[[1]]$z), stringsAsFactors = TRUE)
 
-            p<-peakplot(data[[k]]$peptideSequence, spec=data[[k]], 
+            p <- peakplot(data[[k]]$peptideSequence, spec=data[[k]], 
                 main=paste("scantype: ETD / peptide sequence: ",
                         .PTM_MarkerFinder_(data[[k]]$peptideSequence, data[[k]]$modification, modificationName), sep=''),
                 fi=fi.cyz,
@@ -328,7 +328,7 @@ PTM_MarkerFinder <- function(data,
     close.screen(all.screens = TRUE)
 
     # TODO(cp): make a S3 class
-    rr <- as.data.frame(rr)
+    rr <- as.data.frame(rr, stringsAsFactors = TRUE)
 
     rr$markerIonIntensity <- as.numeric(levels(rr$markerIonIntensity))[rr$markerIonIntensity]
     rr$mZ <- as.numeric(levels(rr$mZ))[rr$mZ]

diff --git a/inst/NEWS.Rd b/inst/NEWS.Rd
@@ -3,8 +3,9 @@
 \newcommand{\ghpr}{\href{https://github.com/protViz/protViz/pull/#1}{##1}}
 \newcommand{\ghit}{\href{https://github.com/protViz/protViz/issues/#1}{##1}}
 
-\section{Changes in protViz version 0.6.0 (2020-02-03)}{
+\section{Changes in protViz version 0.6.2 (2020-03-01)}{
   \itemize{
+    \item fix \ghit{11}.
     \item new by labeling using legend with fragment ion ordered by m/z values \ghit{10}.
     \item fix \ghit{9}.
   }

diff --git a/man/PTM_MarkerFinder.Rd b/man/PTM_MarkerFinder.Rd
@@ -161,25 +161,32 @@ Combining Higher-Energy Collision Dissociation and Electron-Transfer/Higher-Ener
             mono=147.035400, avg=NA, desc="Oxidation",
                     unimodAccID=1)
 
-    m <- as.data.frame(rbind(ptm.0, ptm.1, ptm.2))
+    m <- as.data.frame(rbind(ptm.0, ptm.1, ptm.2), stringsAsFactors = TRUE)
 
-    s <- PTM_MarkerFinder(data=HexNAc, modification=m$mono, 
+    S <- PTM_MarkerFinder(data=HexNAc, modification=m$mono, 
         modificationName=m$desc,
         minMarkerIntensityRatio=3,
         itol_ppm=20,
         mZmarkerIons=HexNAc_MarkerIons) 
 
 
-    boxplot(s$markerIonIntensity ~ s$markerIonMZ,
+    boxplot(markerIonIntensity ~ markerIonMZ,
+        data=S,
         log='y',
         main='Summary plot: boxplot of marker ion intensities from all pPTM spectra',
         xlab='markerIon m/z', 
         ylab='log10 based marker ion intensity')
 
     # export
-    w <- reshape(s[,c(1,7,3,4)], direction='wide', 
-        timevar="markerIonMZ", idvar=c('scans','query'))
-
-    write.table(w, file=file.path(tempdir(), "HexNAc_PTM_markerFinder.csv"),
-        sep=',', row.names=FALSE,col.names=TRUE, quote=FALSE)
+    w <- reshape(S[,c(1,7,3,4)],
+        direction='wide', 
+        timevar="markerIonMZ",
+	idvar=c('scans','query'))
+
+    write.table(w,
+        file=file.path(tempdir(), "HexNAc_PTM_markerFinder.csv"),
+        sep=',',
+	row.names=FALSE,
+	col.names=TRUE,
+	quote=FALSE)
 }
diff --git a/man/fetuinLFQ.Rd b/man/fetuinLFQ.Rd
@@ -91,7 +91,7 @@ The data can be derived out of the mzXML files:
 
 
 contained in a 3GBytes compressed tar ball
-\url{https://fgcz-data.uzh.ch/public/fqms.tgz}.
+\url{http://fgcz-data.uzh.ch/public/fqms.tgz} md5=af804e209844d055c0eded716ef9eea8.
 
 The t3pq data can be derived using the code from \url{https://sourceforge.net/projects/fqms/}