Merge branch 'master' of github.com:bartongroup/Proteus

.Rbuildignore

@@ -1,2 +1,4 @@
+^Meta$
+^doc$
 ^.*\.Rproj$
 ^\.Rproj\.user$

.gitignore

@@ -1,3 +1,5 @@
+Meta
+doc
 .Rproj.user
 .Rhistory
 .RData

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: proteus
 Type: Package
 Title: Downstream analysis of the MaxQuant output
-Version: 0.2.8
+Version: 0.2.12
 Depends: R (>= 3.4)
 Authors@R: c(
   person("Marek", "Gierlinski", email="[email protected]", role=c("aut", "cre")),
@@ -16,7 +16,7 @@ URL: https://github.com/bartongroup/Proteus
 License: GPL-2
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.0
+RoxygenNote: 6.1.1
 Imports:
     dplyr,
     reshape2,

R/func.R

@@ -143,9 +143,10 @@ proteusData <- function(tab, metadata, content, pep2prot, peptides, proteins, me
   }
 
   # number of replicates in each condition
-  cnd <- metadata$condition
-  cnd.fac <- as.factor(cnd)
+  cnd <- as.character(metadata$condition)
+  cnd.fac <- factor(cnd)
   nrep <- tapply(cnd, cnd.fac, length) # nice trick
+  metadata$condition <- cnd.fac
 
   pdat <- list(
     tab = tab,
@@ -257,9 +258,11 @@ readColumnNames <- function(file) {
 #' @return Data frame with selected columns from the evidence file.
 #'
 #' @examples
+#' \dontrun{
 #' library(proteusLabelFree)
 #' evidenceFile <- system.file("extdata", "evidence.txt.gz", package="proteusLabelFree")
 #' evi <- readEvidenceFile(evidenceFile)
+#' }
 #'
 #' @export
 readEvidenceFile <- function(file, measure.cols=measureColumns, data.cols=evidenceColumns, zeroes.are.missing=TRUE) {
@@ -445,9 +448,11 @@ parameterString <- function(...) {
 #'   metadata.
 #'
 #' @examples
+#' \dontrun{
 #' library(proteusLabelFree)
 #' data(proteusLabelFree)
 #' pepdat <- makePeptideTable(evi, meta, ncores=2)
+#' }
 #'
 #' @export
 makePeptideTable <- function(evi, meta, sequence.col=c("sequence", "modified_sequence"),
@@ -459,6 +464,12 @@ makePeptideTable <- function(evi, meta, sequence.col=c("sequence", "modified_seq
   protein.col <- match.arg(protein.col)
   experiment.type <- match.arg(experiment.type)
 
+  # mclapply doesn't work on Windows, so force 1 core
+  if(Sys.info()[['sysname']] == "Windows") {
+    ncores <- 1
+    warning("Multicore processing not available in Windows. Using ncores=1")
+  }
+
   # check if measure.cols, sequence.col and protein.col are in the evidence file
   measures <- names(measure.cols)
   for(col in c(measures, sequence.col, protein.col)) {
@@ -604,6 +615,12 @@ makeProteinTable <- function(pepdat, aggregate.fun=aggregateHifly, ...,
                              min.peptides=2, ncores=4) {
   if(!is(pepdat, "proteusData")) stop ("Input data must be of class proteusData.")
 
+  # mclapply doesn't work on Windows, so force 1 core
+  if(Sys.info()[['sysname']] == "Windows") {
+    ncores <- 1
+    warning("Multicore processing not available in Windows. Using ncores=1")
+  }
+
   meta <- pepdat$metadata
   tab <- pepdat$tab
 

R/live.R

@@ -132,6 +132,7 @@ jitterPlot <- function(tab, input, pdat, max_points) {
         {if(n > 1) geom_errorbar(position=pd, width = 0.1)} +
         scale_shape_identity() +  # necessary for shape mapping
         viridis::scale_fill_viridis(discrete=TRUE) +
+        theme(axis.text.x = element_text(angle = 90, hjust = 1, vjust=0.5)) +
         {if (input$intensityScale == 'Log') labs(x = 'Condition', y = 'Log Intensity') else labs(x = 'Condition', y = 'Intensity')}
     }
   })

README.md

@@ -7,9 +7,9 @@
 Proteus can be installed directly from GitHub. First, you need to install BioConductor and limma:
 
 ```r
-source("https://bioconductor.org/biocLite.R")
-biocLite()
-biocLite("limma")
+install.packages("BiocManager")
+BiocManager::install()
+BiocManager::install("limma")
 ```
 
 You also need devtools:
@@ -29,7 +29,7 @@ devtools::install_github("bartongroup/proteusSILAC")
 Finally, you can install proteus:
 
 ```r
-devtools::install_github("bartongroup/Proteus", build_vignettes = TRUE)
+devtools::install_github("bartongroup/Proteus", build_opts= c("--no-resave-data", "--no-manual"), build_vignettes=TRUE)
 ```
 
 Note: use `build_vignettes = FALSE` if you run into problems with vignettes installation.
@@ -48,3 +48,13 @@ There are additional, shorter vignettes, showing the specifics of using *Proteus
 vignette("TMT", package="proteus")
 vignette("SILAC", package="proteus")
 ```
+
+If, for some reason, you cannot build vignettes, copies are available online:
+
+- [Proteus](http://www.compbio.dundee.ac.uk/user/mgierlinski/proteus/proteus.html)
+- [SILAC](http://www.compbio.dundee.ac.uk/user/mgierlinski/proteus/SILAC.html)
+- [TMT](http://www.compbio.dundee.ac.uk/user/mgierlinski/proteus/TMT.html)
+
+## Application note
+
+The article about this package can be found on [BioRxiv](https://www.biorxiv.org/content/early/2018/09/20/416511).