Venn diagram¶
How to make easy venn (or euler) diagrams of taxa shared or unique to a group of samples
In [1]:
# Package with venn functions
library(MicEco)
In [2]:
# Data
library(phyloseq)
load("../data/physeq.RData")
With counts of shared and unique taxa (ASVs):¶
In [3]:
ps_venn(phy, group = "Time", quantities = list(type=c("counts")))
With percentage of shared and unique:¶
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ps_venn(phy, group = "Time", quantities = list(type=c("percent")))
As an euler diagram¶
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ps_euler(phy, group = "Time", quantities = list(type=c("counts","percent")))
Only include ASVs present in at least 5% of the samples in each group:¶
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ps_euler(phy, group = "Time", quantities = list(type=c("counts")), fraction = 0.05)
Percent is weighted by relative abundance¶
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ps_venn(phy, group = "Time", quantities = list(type=c("percent")), weight = TRUE)
Changing colors etc.¶
In [10]:
ps_venn(phy, group = "Time", fill = c("red", "green", "blue"), alpha = 0.5, quantities = list(type=c("percent"), col = "white"))
