multi_biplot_pq: Visualization of a collection of couples of samples for...

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Visualization of a collection of couples of samples for comparison

Description

This allow to plot all the possible biplot_pq() combination using one factor.

Usage

multi_biplot_pq(physeq, split_by = NULL, pairs = NULL, na_remove = TRUE, ...)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
split_by	(required if pairs is NULL) the name of the factor to make all combination of couples of values
pairs	(required if pairs is NULL) the name of the factor in physeq@sam_data' slot to make plot by pairs of samples. Each level must be present only two times. Note that if you set pairs, you also must set fact arguments to pass on to biplot_pq().
na_remove	(logical, default TRUE) if TRUE remove all the samples with NA in the split_by variable of the physeq@sam_data slot
...	Other parameters passed on to biplot_pq()

Value

a list of ggplot object

Author(s)

Adrien Taudière

Examples

data_fungi_abun <- subset_taxa_pq(data_fungi, taxa_sums(data_fungi) > 10000)
p <- multi_biplot_pq(data_fungi_abun, "Height")
lapply(p, print)

adrientaudiere/MiscMetabar documentation built on Oct. 13, 2024, 9:42 p.m.