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Plot pre-rarefaction diagnostics

Source: R/plot_rarefaction_metrics.R
plot_rarefaction_metrics.Rd

This function creates a 6-panel diagnostic plot showing sequencing depth, Good's coverage, and outlier behavior based on a data frame or a phyloseq object with rare stats already added via add_rare_stats().

Usage

plot_rarefaction_metrics(data)

Arguments

data

Either a phyloseq object or a data.frame that includes columns read_num, goods_cov, and outlier.

Value

A ggarrange object with six plots.

See also

add_rarefaction_metrics()

Examples

library(phyloseq)
library(BRCore)

# Add rarefaction metrics to the phyloseq object
bcse_metrics <- add_rarefaction_metrics(bcse)

# Plot the rarefaction diagnostics
plot_rarefaction_metrics(bcse_metrics)
#> ℹ Processing 50 samples
#> ℹ Generating rarefaction diagnostic plots
#> ✔ Rarefaction diagnostic plots generated successfully
#> ℹ Generating rarefaction diagnostic plots

#> ✔ Generating rarefaction diagnostic plots [878ms]
#> 


# You can also pass a data frame directly if you have
# pre-computed read_num, goods_cov, and outlier columns
sample_data_df <- data.frame(sample_data(bcse_metrics))
plot_rarefaction_metrics(sample_data_df)
#> ℹ Processing 50 samples
#> ℹ Generating rarefaction diagnostic plots
#> ✔ Rarefaction diagnostic plots generated successfully
#> ℹ Generating rarefaction diagnostic plots

#> ✔ Generating rarefaction diagnostic plots [825ms]
#>