Plot Top Abundant Taxa

plotTopAbundant(x, taxa_level = "Family", top = 10L, ...)

Arguments

x: phyloseq object
taxa_level: Taxonomic level at which features are selected. Abundances are summed up for each of the taxa at this level and then top are selected.
top: Numeric value, how many top taxa_level to return. Default top = 100
...: Options to pass ggplot2::geom_jitter()

Value

A ggplot2 object.

Details

Plot the features with the highest abundance in all samples, at a user specific taxonomic level.

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeUtils

Author

Sudarshan A. Shetty

Examples


library(biomeUtils)
library(biomeViz)
p <- plotTopAbundant(SprockettTHData,
                     taxa_level = "Family",
                     top=10L,
                     alpha = 0.25,
                     shape = 124,
                     color="black",
                     fill = "black",
                     size=3,
                     width = 0.02)
#> Joining, by = "taxa"
print(p)