accu_samp_threshold: Compute the number of sequence to obtain a given proportion...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Compute the number of sequence to obtain a given proportion of ASV in accumulation curves

Description

Usage

accu_samp_threshold(res_accuplot, threshold = 0.95)

Arguments

res_accuplot	the result of the function accu_plot()
threshold	the proportion of ASV to obtain in each samples

Value

a value for each sample of the number of sequences needed to obtain threshold proportion of the ASV

Author(s)

Adrien Taudière

See Also

accu_plot()

Examples

data("GlobalPatterns", package = "phyloseq")
GP <- subset_taxa(GlobalPatterns, GlobalPatterns@tax_table[, 1] == "Archaea")
GP <- rarefy_even_depth(subset_samples_pq(GP, sample_sums(GP) > 3000))
p <- accu_plot(GP, "SampleType", add_nb_seq = TRUE, by.fact = TRUE, step = 10)

val_threshold <- accu_samp_threshold(p)

summary(val_threshold)

# Plot the number of sequences needed to accumulate 0.95% of ASV in 50%, 75%
# and 100% of samples
p + geom_vline(xintercept = quantile(val_threshold, probs = c(0.50, 0.75, 1)))

adrientaudiere/MiscMetabar documentation built on May 1, 2024, 6:22 a.m.