holobiont (version 0.1.3)

coreVenn: Venn Diagram Comparing (Non-Phylogenetic) Core Microbiomes from Multiple Habitats

Description

Generates a Venn diagram comparing and contrasting the shared and unique taxa of core microbiomes from two or more (up to seven) different types of habitats using a non-phylogenetic approach.

Usage

coreVenn(x, grouping, core_fraction = 0.5, ab_threshold1 = 0,
ab_threshold2 = 0, ab_threshold3 = 0, selection='basic', max_tax = NULL,
increase_cutoff = 2,ordered_groups=NULL,show_percentage=TRUE,decimal=2,
fill_color=c('red','orange','yellow','green','blue','purple','black'),fill_alpha=0.5,
stroke_color='black',stroke_alpha = 1, stroke_size = 1,stroke_linetype = "solid",
set_name_color = "black", set_name_size = 6,text_color = "black",text_size = 4)

Value

This function returns a plot of the Venn diagram.

Arguments

x

(Required) Microbial community data. This must be in the form of a phyloseq object and must contain, at a minimum, an OTU abundance table and a phylogeny.

grouping

(Required) A vector specifying which samples belong to which habitat type.

core_fraction

The fraction of samples that a microbial taxon must be found in to be considered part of the 'core' microbiome. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.5.

ab_threshold1

The threshold for mean relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

ab_threshold2

The threshold for maximum relative abundance in any sample. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

ab_threshold3

The threshold for minimum relative abundance across all samples. This variable is only used when selection = 'basic' and is ignored when selection = 'shade'. The default value is 0.

selection

Whether to use thresholds ('basic') or the Shade and Stopnisek method ('shade') to define the core community. The default is 'basic'.

max_tax

The maximum number of branches to add sequentially, as a percentage of the total branches when using the Shade and Stopnisek method. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.

increase_cutoff

The threshold for the percent increase in beta diversity used to identify the taxon at which point adding more taxa yields diminishing returns in explanatory power. This variable is only used when selection = 'shade' and is ignored when selection = 'basic'.

ordered_groups

When provided, specifies the order in which different habitats should be plotted. This order is matched to the color order specified in fill_color (see below).

show_percentage

If TRUE the Venn diagram is shown as percentages of the total branch length in each compartment. If FALSE the Venn diagram is shown as absolute branch lengths.

decimal

The number of decimal points to report in the Venn diagram compartments (either for percentages or absolute branch lengths).

fill_color

A vector specifying the colors to use for each of the different habitats in the Venn diagram. The default is to use the six colors of the rainbow, followed by black.

fill_alpha

The transparency of the fill colors in the Venn diagram.

stroke_color

The color of the outlines in the Venn diagram.

stroke_alpha

The transparency of the outlines in the Venn diagram.

stroke_size

The width of the outlines in the Venn diagram.

stroke_linetype

The style of the outlines in the Venn diagram.

set_name_color

The color of the font used to label each habitat.

set_name_size

The size of the font used to label each habitat

text_color

The color of the font used to report the value in each compartment of the Venn diagram

text_size

The size of the font used to report the value in each compartment of the Venn diagram

Details

coreVenn generates a Venn diagram showing either the percentage of taxa or the taxon count shared between the core communities from all possible combinations of up to seven different habitat types. For more details, see Bewick and Camper (2025).

References

Bewick, S.A. and Benjamin T. Camper. "Phylogenetic Measures of the Core Microbiome" <doi:TBD>

McMurdie, Paul J., and Susan Holmes. "phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data." PloS one 8.4 (2013): e61217.

McMurdie, Paul J., and Susan Holmes. "Phyloseq: a bioconductor package for handling and analysis of high-throughput phylogenetic sequence data." Biocomputing 2012. 2012. 235-246.

Shade, Ashley, and Nejc Stopnisek. "Abundance-occupancy distributions to prioritize plant core microbiome membership." Current opinion in microbiology 49 (2019): 50-58.

Examples

#Test with enterotype dataset
library(phyloseq)
library(ape)
library(phytools)
library(ggplot2)
data(enterotype)

set.seed(1)

#Generate an example tree and label it with the names of the microbial taxa
enterotype_tree<-rtree(length(taxa_names(enterotype)))
enterotype_tree$tip.label<-taxa_names(enterotype)
enterotype_tree$node.label<-as.character(1:1:enterotype_tree$Nnode)

#keep only those samples with gender identified
gendered<-which(!(is.na(sample_data(enterotype)$Gender)))
enterotypeMF<-prune_samples(sample_names(enterotype)[gendered],enterotype)

#Create a phyloseq object with a tree
example_phyloseq<-phyloseq(otu_table(enterotypeMF),phy_tree(as.phylo(enterotype_tree)))

coreVenn(example_phyloseq,grouping=sample_data(enterotypeMF)$Gender)