ps_venn: Make Venn diagram of shared taxa (ASVs, OTUs) across sample...

In Russel88/MicEco: Various functions for microbial community data

Make Venn diagram of shared taxa (ASVs, OTUs) across sample groups

Description

Make Venn diagram of shared taxa (ASVs, OTUs) across sample groups from a phyloseq object. Overlap can be weighted by relative abundance #' Any further arguments to this function are passed to the plot.venn function from the eulerr package. This can be used to change colors, fonts, and other graphical parameters. For example: ps_venn(phy, "Time", quantities = list(type=c("percent","counts"), font = 2), labels = list(cex = 2), col = "red", fill = c("red","blue","green"))

Usage

ps_venn(
  ps,
  group,
  fraction = 0,
  weight = FALSE,
  relative = TRUE,
  plot = TRUE,
  ...
)

Arguments

ps	A phyloseq object
group	The grouping factor. Should match variable in sample_data(ps)
fraction	The fraction (0 to 1) of samples in a group in which the taxa should be present to be included in the count.
weight	If TRUE, the overlaps are weighted by abundance
relative	Should abundances be made relative
plot	If TRUE return a plot, if FALSE return a list with shared and unique taxa
...	Additional arguments

Value

An venn plot

Russel88/MicEco documentation built on Nov. 24, 2022, 2:33 a.m.