beta_cpcoa_dis: Plotting beta diversity scatter plot of Constrained PCoA

In microbiota/amplicon: Statistics and visualization for microbiome data

Plotting beta diversity scatter plot of Constrained PCoA

Description

Input distance matrix and metadata, and manual set metadata column names. ggplot2 show CPCoA with color and stat ellipse.

Usage

beta_cpcoa_dis(
  distance_mat,
  metadata,
  groupID = "genotype",
  ellipse = T,
  label = F
)

Arguments

metadata	matrix or dataframe, including sampleID and groupID;
groupID	column name for groupID.
ellipse	stat ellipse, T or F.
label	sample name showing, T or F.
dis	distance type for caucluate, default "bray_curtis", alternative "unifrac, unifrac_binary, jaccard、manhatten, euclidean".

Details

By default, returns beta CPCoA coordinate The available diversity indices include the following:

• most used indices: bray_curtis, unifrac, unifrac_binary, jaccard

• other used indices: manhatten, euclidean

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

beta_cpcoa_dis

Examples

# example data: OTU table, rownames is OTU_xxx, colnames is SampleID
data(beta_bray_curtis)
# example data: metadata or design, include SampleID, genotype and site
data(metadata)
# Set 2 parameters: otu table, metadata, and distance type and groupID using default "bray_curtis" and "genotype"
beta_cpcoa_dis(beta_bray_curtis, metadata)
# Set 3 parameters: distance matrix, metadata, and groupID as "site"
beta_cpcoa_dis(beta_bray_curtis, metadata, "site")
# Set 5 parameters: distance matrix, metadata, and groupID as using "genotype", open stat elipse and sample label
beta_cpcoa_dis(beta_bray_curtis, metadata, groupID = "genotype", ellipse = T, label = T)

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