get_vennlist: generate a vennlist for VennDiagram

In MicrobiotaProcess: an R package for analysis, visualization and biomarker discovery of microbiome

Description

generate a vennlist for VennDiagram

Usage

get_vennlist(obj, ...)

## S4 method for signature 'phyloseq'
get_vennlist(obj, factorNames, ...)

## S4 method for signature 'data.frame'
get_vennlist(obj, sampleinfo = NULL, factorNames = NULL, ...)

Arguments

obj	phyloseq, phyloseq class or data.frame a dataframe contained one character column and the others are numeric. or all columns should be numeric if sampleinfo isn't NULL.
...,	additional parameters
factorNames	character, a column name of sampleinfo, when sampleinfo isn't NULL, factorNames shouldn't be NULL, default is NULL, when the input is phyloseq, the factorNames should be provided.
sampleinfo	dataframe; a sample information, default is NULL.

Value

return a list for VennDiagram.

Author(s)

Shuangbin Xu

Examples

data(test_otu_data)
vennlist <- get_vennlist(test_otu_data, 
                 factorNames="group")
vennlist
#library(VennDiagram)
#venn.diagram(vennlist, height=5, 
#             width=5, filename = "./test_venn.pdf", 
#             alpha = 0.85, fontfamily = "serif", 
#             fontface = "bold",cex = 1.2, 
#             cat.cex = 1.2, cat.default.pos = "outer",
#             cat.dist = c(0.22,0.22,0.12,0.12), 
#             margin = 0.1, lwd = 3, 
#             lty ='dotted', 
#             imagetype = "pdf")

MicrobiotaProcess documentation built on April 18, 2021, 6 p.m.