From 67b93ea9549e6301819156565d9410f2c08a0885 Mon Sep 17 00:00:00 2001
From: Jakob Russel <cmf483@science.domain>
Date: Wed, 19 Feb 2020 12:42:11 +0100
Subject: [PATCH] new version

---
 DESCRIPTION        |  4 ++--
 NAMESPACE          |  6 ++++++
 R/phylo_euler.R    | 40 ++++++++++++++++++++++++++++++++++++++++
 R/ps_refactor.R    |  1 +
 README.md          |  5 +++++
 man/phylo_euler.Rd | 30 ++++++++++++++++++++++++++++++
 6 files changed, 84 insertions(+), 2 deletions(-)
 create mode 100644 R/phylo_euler.R
 create mode 100644 man/phylo_euler.Rd

diff --git a/DESCRIPTION b/DESCRIPTION
index a74ff78..bb9bbd4 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: MicEco
 Title: Various functions for microbial community data
-Version: 0.9.5
+Version: 0.9.6
 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, reshape2
+Imports: stats, utils, phyloseq, foreach, doSNOW, picante, vegan, snow, bbmle, Hmisc, abind, reshape2, eulerr
 License: GPL (>= 3) | file LICENSE
 Encoding: UTF-8
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index c1afa76..2329f51 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -7,6 +7,7 @@ export(comdistnt.par)
 export(community_rrna)
 export(neutral.fit)
 export(neutral.rand)
+export(phylo_euler)
 export(proportionality)
 export(ps_refactor)
 export(rarefy_rrna)
@@ -24,6 +25,7 @@ export(ses.permtest)
 import(Hmisc)
 import(bbmle)
 import(doSNOW)
+import(eulerr)
 import(foreach)
 import(parallel)
 import(phyloseq)
@@ -32,9 +34,13 @@ import(utils)
 import(vegan)
 importFrom(abind,abind)
 importFrom(reshape2,dcast)
+importFrom(stats,aggregate)
 importFrom(stats,as.dist)
+importFrom(stats,as.formula)
 importFrom(stats,cov)
+importFrom(stats,dist)
 importFrom(stats,dnorm)
+importFrom(stats,hclust)
 importFrom(stats,na.omit)
 importFrom(stats,p.adjust)
 importFrom(stats,pbeta)
diff --git a/R/phylo_euler.R b/R/phylo_euler.R
new file mode 100644
index 0000000..6ea3084
--- /dev/null
+++ b/R/phylo_euler.R
@@ -0,0 +1,40 @@
+#' Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups
+#'
+#' Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
+#' @param ps A phyloseq object
+#' @param group The grouping factor. Should match variable in sample_data(ps)
+#' @param weight If TRUE, the overlaps are weighted by abundance
+#' @param type "percent" or "count"
+#' @param relative Should abundances be made relative
+#' @param ... Additional arguments
+#' @keywords venn euler diagram
+#' @return An euler plot
+#' @import phyloseq
+#' @import eulerr
+#' @importFrom stats aggregate as.formula
+#' @export
+
+phylo_euler <- function(ps, group, weight = FALSE, type = "percent", relative = TRUE, ...){
+    
+    if(relative){
+        ps <- transform_sample_counts(ps, function(x) x/sum(x))
+    }
+    
+    ps_melted <- psmelt(ps)
+    
+    ps_agg <- aggregate(as.formula(paste("Abundance ~ OTU +",group)), data = ps_melted, function(x) mean(x))
+    
+    ps_mat <- reshape2::dcast(as.formula(paste("OTU ~ ",group)), data = ps_agg, value.var = "Abundance")
+    
+    ps_mat <- ps_mat[, -1]
+    ps_mat_bin <- (ps_mat>0)*1
+    
+    if(weight){
+        df <- euler(ps_mat_bin, weights = rowMeans(ps_mat))
+    } else {
+        df <- euler(ps_mat_bin)
+    }
+    
+    plot(df, quantities = list(type=type), ...)
+    
+}
\ No newline at end of file
diff --git a/R/ps_refactor.R b/R/ps_refactor.R
index 849800f..4da9f8c 100644
--- a/R/ps_refactor.R
+++ b/R/ps_refactor.R
@@ -6,6 +6,7 @@
 #' @param psmelted A phyloseq object melted into a data.frame with psmelt
 #' @param ... Arguments passed to hclust
 #' @importFrom reshape2 dcast
+#' @importFrom stats dist hclust
 #' @export
 ps_refactor <- function(psmelted, ...){
     if(!is(psmelted, "data.frame")){
diff --git a/README.md b/README.md
index d578143..420de15 100644
--- a/README.md
+++ b/README.md
@@ -12,6 +12,11 @@ MicEco: Various functions for analysis for microbial community data
 ### Citation
 [![DOI](https://zenodo.org/badge/83547545.svg)](https://zenodo.org/badge/latestdoi/83547545)
 
+
+#### phylo_euler
+
+Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
+
 #### adonis_OmegaSq
 
 Calculate the unbiased effect size estimation (partial) omega-squared for adonis (PERMANOVA) models
diff --git a/man/phylo_euler.Rd b/man/phylo_euler.Rd
new file mode 100644
index 0000000..6a713e0
--- /dev/null
+++ b/man/phylo_euler.Rd
@@ -0,0 +1,30 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/phylo_euler.R
+\name{phylo_euler}
+\alias{phylo_euler}
+\title{Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups}
+\usage{
+phylo_euler(ps, group, weight = FALSE, type = "percent", relative = TRUE, ...)
+}
+\arguments{
+\item{ps}{A phyloseq object}
+
+\item{group}{The grouping factor. Should match variable in sample_data(ps)}
+
+\item{weight}{If TRUE, the overlaps are weighted by abundance}
+
+\item{type}{"percent" or "count"}
+
+\item{relative}{Should abundances be made relative}
+
+\item{...}{Additional arguments}
+}
+\value{
+An euler plot
+}
+\description{
+Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
+}
+\keyword{diagram}
+\keyword{euler}
+\keyword{venn}