Description Usage Arguments Details Value Author(s) Examples
View source: R/plot_taxa_prevalence.R
Create taxa prevalence plots at various taxonomic levels.
1 | plot_taxa_prevalence(x, level, detection = 0)
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x |
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level |
Phylum/Order/Class/Family |
detection |
Detection threshold for presence (prevalance) |
This helps to obtain first insights into how is the taxa distribution in the data. It also gives an idea about the taxonomic affiliation of rare and abundant taxa in the data. This may be helpful for data filtering or other downstream analysis.
A ggplot
plot object.
Sudarshan A. Shetty sudarshanshetty9@gmail.com
1 2 3 4 5 6 7 | data(atlas1006)
# Pick data subset just to speed up example
p0 <- subset_samples(atlas1006, DNA_extraction_method == "r")
p0 <- prune_taxa(taxa(p0)[grep("Bacteroides", taxa(p0))], p0)
# Detection threshold (0 by default; higher especially with HITChip)
p <- plot_taxa_prevalence(p0, 'Phylum', detection = 1)
print(p)
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