tax_maptree: Plotting maptree of taxonomy

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting maptree of taxonomy

Description

Visualize mapdata. Finally, return a ggplot2 object.

Usage

tax_maptree(x)

Arguments

mapdata

format2maptree result

Details

By default, returns mapadd[1] is ggplot object The available style include the following:

• phylum: color by phylum

• diff: color by diff

Value

ggplot2 object.

Author(s)

Contact: Tao Wen, 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

data_to_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.