Merge pull request #202 from lgatto/reshape2

remove reshape2; see #201

Author: LaurentGatto

Diff for: DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MSnbase
 Title: Base Functions and Classes for Mass Spectrometry and Proteomics
-Version: 2.1.14
+Version: 2.1.15
 Description: Manipulation, processing and visualisation
     of mass spectrometry and proteomics data.
 Authors@R: c(person(given = "Laurent", family = "Gatto",
@@ -52,7 +52,6 @@ Imports:
     preprocessCore,
     vsn,
     grid,
-    reshape2,
     stats4,
     affy,
     impute,

Diff for: NAMESPACE

@@ -32,8 +32,6 @@ importFrom(ggplot2, geom_histogram, geom_text, geom_line, geom_point,
            scale_x_continuous, scale_x_log10, coord_cartesian,
            facet_grid)
 
-import(reshape2) ## try to reduce this
-
 importFrom(MALDIquant, binPeaks, match.closest) ## only using ::: functions
 importFrom(S4Vectors, isEmpty, metadata)
 

Diff for: NEWS.md

@@ -1,5 +1,8 @@
 # MSnbase 2.1
 
+## Changes in version 2.1.15
+- Remove reshape2 dependency; see #201 <2017-04-06 Thu>
+
 ## Changes in version 2.1.14
 - Internal rewrite and speedup of topN; Briefly multiple apply calls are
   avoided, `getTopIdx` and `subsetById` are replaced by `.topIdx`.

Diff for: R/functions-mzR.R

@@ -68,8 +68,8 @@ plotMzDelta_list <- function(object,            ## peakLists
     }
     delta <- unlist(delta)
     ## could round deltas to speed up?
-    delta <- melt(delta)
-    p <- ggplot(delta, aes(x = value)) + 
+    delta <- data.frame(value = delta)
+    p <- ggplot(delta, aes(x = value)) +
         geom_histogram(aes(y = ..density..), stat = "bin", binwidth = bw) +
             scale_x_continuous(limits = xlim) +
                     xlab("m/z delta") + ylab("Density") +

Diff for: R/methods-MSnSet.R

@@ -451,10 +451,10 @@ setMethod("image", "MSnSet",
               ## get rid of 'no visible global function definition' note
               sample.name <- feature.id <- Expression <- NULL
               isFC <- any(exprs(x) < 0, na.rm = TRUE)
-              xlong <- melt(exprs(x))
-              colnames(xlong) <- c("feature.id", "sample.name", "Expression")
-              xlong[['feature.id']] <- as.character(xlong[['feature.id']])
-              xlong[['sample.name']] <- as.character(xlong[['sample.name']])
+              xlong <- cbind(expand.grid("feature.id" = featureNames(x),
+                                         "sample.name" = sampleNames(x),
+                                         stringsAsFactors=FALSE),
+                             "Expression" = as.vector(exprs(x)))
               xlong <- merge(xlong, fData(x), by.x = "feature.id", by.y = 0)
               xlong <- merge(xlong, pData(x), by.x = "sample.name", by.y = 0)
               x <- xlong

Diff for: R/missing-data.R

@@ -24,7 +24,9 @@
 plotNA_matrix <- function(X, pNA) {
   pNA <- pNA[1]
   dfr1 <- .preparePlotNAData(X)
-  dfr2 <- melt(dfr1, measure.vars=c("proteins", "data"))
+  dfr2 <- data.frame(x = 1:nrow(dfr1),
+                     variable = rep(c("proteins", "data"), each = nrow(dfr1)),
+                     value = c(dfr1$proteins, dfr1$data))
   nkeep <- sum(dfr1$proteins >= (1 - pNA))
   kkeep <- dfr1$data[nkeep]
   x <- y <- z <- value <- variable <- NULL

Diff for: R/plotting-MSnExp.R

@@ -102,8 +102,7 @@ plotMzDelta_MSnExp <- function(object,            ## MSnExp object
         close(pb)
         message(" Plotting...\n")
     }
-    delta <- unlist(delta)
-    delta <- melt(delta)
+    delta <- data.frame(value = unlist(delta))
     p <- ggplot(delta, aes(x = value)) +
         geom_histogram(aes(y = ..density..), stat = "bin", binwidth = bw) +
             scale_x_continuous(limits = xlim) +