update

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: MicEco
 Title: Various functions for microbial community data
-Version: 0.9.4
+Version: 0.9.5
 Authors@R: person("Jakob", "Russel", email = "russel2620@gmail.com", role = c("aut", "cre"))
 Description: Collection of functions for microbiome analyses. E.g. fitting neutral models and standardized effect sizes of phylogenetic beta diversities, and much more.
 Depends: R (>= 3.2.5)
-Imports: stats, utils, phyloseq, foreach, doSNOW, picante, vegan, snow, bbmle, Hmisc, abind
+Imports: stats, utils, phyloseq, foreach, doSNOW, picante, vegan, snow, bbmle, Hmisc, abind, reshape2
 License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
 Remotes: bioc::release/phyloseq

NAMESPACE

@@ -8,6 +8,7 @@ export(community_rrna)
 export(neutral.fit)
 export(neutral.rand)
 export(proportionality)
+export(ps_refactor)
 export(rarefy_rrna)
 export(rarefy_rrna.matrix)
 export(rarefy_rrna.phyloseq)
@@ -30,6 +31,7 @@ import(picante)
 import(utils)
 import(vegan)
 importFrom(abind,abind)
+importFrom(reshape2,dcast)
 importFrom(stats,as.dist)
 importFrom(stats,cov)
 importFrom(stats,dnorm)

R/ps_refactor.R

@@ -0,0 +1,18 @@
+#' Relevel the Sample variable in a psmelted phyloseq object 
+#' 
+#' Relevel the Sample variable in a psmelted phyloseq object, 
+#' such that similar samples are plotted together with ggplot barcharts 
+#' 
+#' @param psmelted A phyloseq object melted into a data.frame with psmelt
+#' @param ... Arguments passed to hclust
+#' @importFrom reshape2 dcast
+#' @export
+ps_refactor <- function(psmelted, ...){
+    if(!is(psmelted, "data.frame")){
+        stop("Input should be a phyloseq object melted into a data.frame with psmelt")
+    }
+    mat <- reshape2::dcast(OTU ~ Sample, value.var = "Abundance", data = psmelted)   
+    hc <- hclust(dist(t(mat[, -1])), ...)
+    psmelted$Sample <- factor(psmelted$Sample, levels = hc$labels[hc$order])
+    return(psmelted)
+}    

README.md

@@ -20,6 +20,10 @@ Calculate the unbiased effect size estimation (partial) omega-squared for adonis
 
 Rarefaction curve (theoretical and fast) from a phyloseq object. Output ready for plotting in ggplot2
 
+#### ps_refactor
+
+Relevel the Sample variable in a psmelted phyloseq object, such that similar samples are plotted together with ggplot barcharts.
+
 #### UniFrac.multi
 
 With unrooted phylogenies UniFrac sets the root randomly on the tree.