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Rarefy (equalize) the number of samples per modality of a factor

Source: R/dada_phyloseq.R
rarefy_sample_count_by_modality.Rd

lifecycle-experimental

This function randomly draw the same number of samples for each modality of factor. It is usefull to dissentangle the effect of different number of samples per modality on diversity. Internally used in accu_plot_balanced_modality().

Usage

rarefy_sample_count_by_modality(physeq, fact, rngseed = FALSE, verbose = TRUE)

Arguments

physeq

(required): a phyloseq-class object obtained using the phyloseq package.

fact

(required): The variable to rarefy. Must be present in the sam_data slot of the physeq object.

rngseed

(Optional). A single integer value passed to set.seed, which is used to fix a seed for reproducibly random number generation (in this case, reproducibly random subsampling). If set to FALSE, then no iddling with the RNG seed is performed, and it is up to the user to appropriately call

verbose

(logical). If TRUE, print additional informations.

Value

A new phyloseq-class object.

See also

accu_plot_balanced_modality()

Author

Adrien Taudière

Examples

table(data_fungi_mini@sam_data$Height)
#> 
#>   High    Low Middle 
#>     28     32     30 
data_fungi_mini2 <- rarefy_sample_count_by_modality(data_fungi_mini, "Height")
#> You set `rngseed` to FALSE. Make sure you've set & recorded
#>  the random seed of your session for reproducibility.
#> See `?set.seed`
#> ...
table(data_fungi_mini2@sam_data$Height)
#> 
#>   High    Low Middle 
#>     28     28     28 
if (requireNamespace("patchwork")) {
  ggvenn_pq(data_fungi_mini, "Height") + ggvenn_pq(data_fungi_mini2, "Height")
}
#> Taxa are now in columns.
#> Taxa are now in columns.