Description Usage Arguments Details Value Examples
View source: R/universal_microbes.R
Identify and plot "universal" interactions at the designated taxonomic level
1 2 3 4 5 | get_universal_interactions(
tax_level = "ASV",
show_plot = FALSE,
order_by = "abundance"
)
|
tax_level |
taxonomic level at which to agglomerate data |
show_plot |
show() plot in addition to rendering it to a file |
order_by |
ordering of bigraph components; options are "abundance" or "taxonomy" |
Correlations are evaluated in the CLR. A threshold of 0.4 will identify pairs of taxa with median correlation of > 0.4 or < -0.4. Pairs are rendered as bigraphs.
data.frame of microbial pairs (by index in taxonomy and label) and median correlation across hosts
1 | interaction_matrix <- get_universal_interactions(tax_level="ASV")
|
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