tax_circlize: Plotting circlize of taxonomy for groups or samples

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting circlize of taxonomy for groups or samples

Description

Input taxonomy composition, and metadata (SampleID and groupID). Then select top N high abundance taxonomy and group other low abundance. When Select samples can draw sample composition by facet groups. If used group can show mean of each group. Finally, return a ggplot2 object.

Usage

tax_circlize(tax_sum, metadata, topN = 5, groupID = "Group")

Arguments

tax_sum	composition matrix, like OTU table and rowname is taxonomy, typical output of usearch -sintax_summary;
metadata	matrix or dataframe, including sampleID and groupID;
topN	Top N taxonomy to show, default 8, alternative 4, 6, 10 ...;
groupID	column name for groupID;
style	group or sample, default group
sorted	Legend sorted type, default abundance, alternative alphabet

Details

By default, returns top 8 taxonomy and group mean stackplot The available style include the following:

• group: group mean circlize

• sample: each sample circlize

Value

ggplot2 object.

Author(s)

Contact: 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, DOI: https://doi.org/10.1007/s13238-020-00724-8

Jingying Zhang, Yong-Xin Liu, Na Zhang, Bin Hu, Tao Jin, Haoran Xu, Yuan Qin, Pengxu Yan, Xiaoning Zhang, Xiaoxuan Guo, Jing Hui, Shouyun Cao, Xin Wang, Chao Wang, Hui Wang, Baoyuan Qu, Guangyi Fan, Lixing Yuan, Ruben Garrido-Oter, Chengcai Chu & Yang Bai. NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice. Nature Biotechnology, 2019(37), 6:676-684, DOI: https://doi.org/10.1038/s41587-019-0104-4

See Also

tax_circlize

Examples

# Taxonomy table in phylum level, rownames is Phylum, colnames is SampleID
data(tax_phylum)
# metadata, include SampleID, Group and Site
data(metadata)
# Set 4 parameters: set top 5 taxonomy, group by "Group"
tax_circlize(tax_sum = tax_phylum, metadata, topN = 5, groupID = "Group")

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