format2maptree: Format feature table and taxonomy into maptree data

In microbiota/amplicon: Statistics and visualization for microbiome data

Format feature table and taxonomy into maptree data

Description

Input taxonomy composition, and feature table. Then select top N high abundance features.Finally, return a maptree(ggraph) object.

Usage

format2maptree(otu = otutab, tax = taxonomy, N = 200)

Arguments

otu	OTU/ASV table;
tax	taxonomy annotation, include feature ID and 7 levels;
N	Top N features to show, default 200;

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

Zhang, J., Zhang, N., Liu, Y.X., Zhang, X., Hu, B., Qin, Y., Xu, H., Wang, H., Guo, X., Qian, J., et al. (2018). Root microbiota shift in rice correlates with resident time in the field and developmental stage. Sci China Life Sci 61, DOI: https://doi.org/10.1007/s11427-018-9284-4

See Also

tax_maptree

Examples

# Input feature table, taxonomy and Top N features, and format into mapdata
mapdata = format2maptree(otutab, taxonomy, 200)
# Add mean abundance size and phylum color for maptree
mapadd = tax_maptree(mapdata)
# Saving and plotting maptree
(p = mapadd[[1]])

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