amp_venn | R Documentation |
Calculates the number of "core" OTUs shared by groups given thresholds for how frequent the OTUs should be above a certain abundance. Also returns the average abundance of the OTUs in a particular group.
amp_venn(
data,
group_by = NULL,
cut_a = 0.1,
cut_f = 80,
text_size = 5,
normalise = TRUE,
detailed_output = FALSE
)
data |
(required) Data list as loaded with |
group_by |
Group the data based on a sample metadata variable. |
cut_a |
Abundance cutoff in percent. OTU's below this abundance are excluded from the analysis. (default: |
cut_f |
Frequency cutoff in percent. OTU's within the top |
text_size |
Size of the plotted text. (default: |
normalise |
(logical) Normalise the OTU read counts to be in percent per sample. (default: |
detailed_output |
(logical) Return additional details or not. If |
A ggplot2 object.
See ?amp_filter_samples
or the ampvis2 FAQ.
Kasper Skytte Andersen ksa@bio.aau.dk
Mads Albertsen MadsAlbertsen85@gmail.com
[Saunders et al, 2016](https://www.nature.com/articles/ismej2015117)
amp_load
# Load example data
data("AalborgWWTPs")
# Venn diagram grouped by WWTP
amp_venn(AalborgWWTPs, group_by = "Plant")
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