get_vennlist {MicrobiotaProcess} | R Documentation |
generate a vennlist for VennDiagram
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, ...)
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. |
return a list for VennDiagram.
Shuangbin Xu
## Not run: data(test_otu_data) test_otu_data %<>% as.phyloseq() 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") ## End(Not run)