venn_pq: Venn diagram of 'phyloseq-class' object

In adrientaudiere/MiscMetabar: Miscellaneous Functions for Metabarcoding Analysis

Venn diagram of phyloseq-class object

Description

Graphical representation of distribution of taxa across combined modality of a factor.

Usage

venn_pq(physeq, fact, min_nb_seq = 0, print_values = TRUE)

Arguments

physeq	(required): a phyloseq-class object obtained using the phyloseq package.
fact	(required): Name of the factor to cluster samples by modalities. Need to be in physeq@sam_data.
min_nb_seq	(default: 0)): minimum number of sequences by OTUs by samples to take into count this OTUs in this sample. For example, if min_nb_seq=2,each value of 2 or less in the OTU table will be change into 0 for the analysis
print_values	(logical) Print (or not) the table of number of OTUs for each combination. If print_values is TRUE the object is not a ggplot object. Please use print_values = FALSE if you want to add ggplot function (cf example).

Value

A ggplot2 plot representing Venn diagram of modalities of the argument factor

Author(s)

Adrien Taudière

See Also

venneuler

Examples

if (requireNamespace("venneuler")) {
  data("enterotype")
  venn_pq(enterotype, fact = "SeqTech")
}

if (requireNamespace("venneuler")) {
  venn_pq(enterotype, fact = "ClinicalStatus")
  venn_pq(enterotype, fact = "Nationality", print_values = FALSE)
  venn_pq(enterotype, fact = "ClinicalStatus", print_values = FALSE) +
    scale_fill_hue()
  venn_pq(enterotype, fact = "ClinicalStatus", print_values = FALSE) +
    scale_fill_hue()
}

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