1.13.3 update psmelt, pr/489

Author: joey711

.gitignore

@@ -1,6 +1,7 @@
 *.DS_Store
 *.Rhistory
 *.Rproj
+*Rplots.pdf
 
 cache/*
 figure/*

DESCRIPTION

@@ -2,7 +2,7 @@ Package: phyloseq
 Version: 1.13.3
 Date: 2015-06-17
 Title: Handling and analysis of high-throughput microbiome
-    census data.
+    census data
 Description: phyloseq provides a set of classes and tools
     to facilitate the import, storage, analysis, and
     graphical display of microbiome census data.
@@ -33,6 +33,7 @@ Depends:
     R (>= 3.1.0)
 Suggests:
     genefilter (>= 1.42.0),
+    reshape (>= 0.8.5),
     testthat (>= 0.8),
     knitr (>= 1.3)
 VignetteBuilder: knitr

R/plot-methods.R

@@ -1469,7 +1469,7 @@ psmelt = function(physeq){
   otutab = otu_table(physeq)
   if(!taxa_are_rows(otutab)){otutab <- t(otutab)}
   # Melt the OTU table: wide form to long form table
-  mdf = melt(as(otutab, "matrix"))
+  mdf = reshape2::melt(as(otutab, "matrix"))
   colnames(mdf)[1] <- "OTU"
   colnames(mdf)[2] <- "Sample"
   colnames(mdf)[3] <- "Abundance"

README.md

@@ -14,12 +14,15 @@ Presubmission versions ahead of acceptance (2013):
 
 
 ## Latest peer-reviewed article about phyloseq
+
 [phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data](http://dx.plos.org/10.1371/journal.pone.0061217) (2013) PLoS ONE 8(4):e61217
 
 ## Interface with microbio.me/qiime
+
 See the [microbio_me_qiime tutorial](http://joey711.github.io/phyloseq/download-microbio.me.html) for more details and examples downloading and importing into phyloseq/R directly from this public database.
 
 ## Other resources
+
 The phyloseq project also has a number of supporting online resources, most of which can by found at [the phyloseq home page](http://joey711.github.com/phyloseq/), or from the phyloseq stable release [page on Bioconductor](http://bioconductor.org/packages/release/bioc/html/phyloseq.html).
 
 To post feature requests or ask for help, try [the phyloseq Issue Tracker](https://github.com/joey711/phyloseq/issues).

tests/testthat/test-plot.R

@@ -499,10 +499,10 @@ test_that("psmelt doesn't break when the number of taxa is 1", {
 })
 test_that("psmelt doesn't break when package reshape is loaded", {
     data(GlobalPatterns)
-    library(reshape)
+    library("reshape")
     mdf1 <- psmelt(GlobalPatterns)
     detach(package:reshape)
     mdf2 <-psmelt(GlobalPatterns)
-    expect_equivalent(mdf1,mdf2)
+    expect_equivalent(mdf1, mdf2)
 })
 ################################################################################