tax_wordcloud: Wordcloud plot relative abundance of taxonomy

In microbiota/amplicon: Statistics and visualization for microbiome data

Wordcloud plot relative abundance of taxonomy

Description

Input otutab, metadata and taxonomy or phyloseq object; plot wordcloud to visualize compositional microbial community data

Usage

tax_wordcloud(
  otu = otutab,
  map = metadata,
  tax = taxonomy,
  ps = NULL,
  j = "Phylum",
  group = "Group",
  facet = F,
  abundance = T,
  rand = 1
)

Arguments

otu	OTU/ASV table;
map	Sample metadata;
tax	taxonomy file;
j	taxonomy annotation classification level, typical including "Phylum","Class","Order","Family","Genus"
group	group ID;
facet	FALSE/F, if TURE/T, facet with Phylum in one of the "Class","Order","Family","Genus" level
abundance	TRUE/T, show abundance in label, turn off in FLASE/F;
rand	set reproducible layout, default 1, can set any integer;

Details

By default, input phyloseq object include metadata, otutab and metadata The available classification level include the following:

• most used classification level was Phylum

• other classification level include: Class, Order, Family, Genus

Value

list object including plot and data table

Author(s)

Contact: Tao Wen [e-mail], Yong-Xin Liu [e-mail]

References

Yong-Xin Liu, Yuan Qin, Tong Chen, Meiping Lu, Xubo Qian, Xiaoxuan Guo & Yang Bai. A practical guide to amplicon and metagenomic analysis of microbiome data. Protein Cell, 2020(41), 1-16, DOI: https://doi.org/10.1007/s13238-020-00724-8

See Also

tax_stackplot tax_circlize tax_maptree

Examples

# Input feature table, metadata, taxonomy, group column name, and taxonomic level
# Output each group Phylum wordcloud with relative abundance in bracket
tax_wordcloud(otu = otutab, map = metadata, tax = taxonomy, group = "Group", j = "Phylum")
# Input feature table, metadata, taxonomy, group column name, and taxonomic level
# in Class, facet by Phylum, not show abundance, layout in seed 2
tax_wordcloud(otu = otutab, map = metadata, tax = taxonomy, group = "Group", j = "Class", facet = T, abundance = F, rand = 2)

microbiota/amplicon documentation built on April 30, 2023, 1:48 p.m.