add ps_venn and change name of phylo_euler

Author: Jakob Russel

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: MicEco
 Title: Various functions for microbial community data
-Version: 0.9.6
+Version: 0.9.7
 Authors@R: person("Jakob", "Russel", email = "[email protected]", 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)

NAMESPACE

@@ -7,9 +7,10 @@ export(comdistnt.par)
 export(community_rrna)
 export(neutral.fit)
 export(neutral.rand)
-export(phylo_euler)
 export(proportionality)
+export(ps_euler)
 export(ps_refactor)
+export(ps_venn)
 export(rarefy_rrna)
 export(rarefy_rrna.matrix)
 export(rarefy_rrna.phyloseq)

R/phylo_euler.R R/ps_euler.RR/phylo_euler.R renamed to R/ps_euler.R

@@ -1,20 +1,20 @@
-#' Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups
+#' Make Euler 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
+#' Make Euler 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 type "percent" or "counts"
 #' @param relative Should abundances be made relative
 #' @param ... Additional arguments
-#' @keywords venn euler diagram
+#' @keywords 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, ...){
+ps_euler <- function(ps, group, weight = FALSE, type = "percent", relative = TRUE, ...){
 
     if(relative){
         ps <- transform_sample_counts(ps, function(x) x/sum(x))
@@ -30,9 +30,9 @@ phylo_euler <- function(ps, group, weight = FALSE, type = "percent", relative =
     ps_mat_bin <- (ps_mat>0)*1
 
     if(weight){
-        df <- euler(ps_mat_bin, weights = rowMeans(ps_mat))
+        df <- eulerr::euler(ps_mat_bin, weights = rowMeans(ps_mat))
     } else {
-        df <- euler(ps_mat_bin)
+        df <- eulerr::euler(ps_mat_bin)
     }
 
     plot(df, quantities = list(type=type), ...)

R/ps_venn.R

@@ -0,0 +1,40 @@
+#' Make Venn diagram of shared taxa (ASVs, OTUs) across sample groups
+#'
+#' Make 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 "counts"
+#' @param relative Should abundances be made relative
+#' @param ... Additional arguments
+#' @keywords venn diagram
+#' @return An venn plot
+#' @import phyloseq
+#' @import eulerr
+#' @importFrom stats aggregate as.formula
+#' @export
+
+ps_venn <- 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 <- eulerr::venn(ps_mat_bin, weights = rowMeans(ps_mat))
+    } else {
+        df <- eulerr::venn(ps_mat_bin)
+    }
+    
+    plot(df, quantities = list(type=type), ...)
+    
+}

README.md

@@ -12,10 +12,13 @@ MicEco: Various functions for analysis for microbial community data
 ### Citation
 [![DOI](https://zenodo.org/badge/83547545.svg)](https://zenodo.org/badge/latestdoi/83547545)
 
+#### ps_venn
 
-#### phylo_euler
+Make Venn diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
 
-Make Euler (Venn) diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
+#### ps_euler
+
+Make Euler diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance
 
 #### adonis_OmegaSq