ordination: Ordination and beta dispersion

In rusher321/microbiotaPair: An R Package for Simplified Microbiome Analysis Workflows on Intervention Study

Ordination and beta dispersion

Description

This function performs ordination using a selected method. It also performs PERMANOVA using a distance matrix corresponding to the taxa abundance under the different conditions/groups. It also computes pairwise beta dispersion for all conditions of a selected grouping variable, beta dispersion is measured as the average distance of group members to the group centroid. The function a solution of ordination, PERMANOVA results and beta dispersion results. See value for details.

Usage

ordination(physeq, method, grouping_column)

Arguments

physeq	(Required). A phyloseq object containing merged information of abundance, taxonomic assignment, sample data including the measured variables and categorical information of the samples, and / or phylogenetic tree if available.
which_distance	(Optional). A string character specifying dissimilarity index to be used in calculating pairwise distances (Default index is "bray".). "unifrac","wunifrac","manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "altGower", "morisita", "horn", "mountford", "raup" , "binomial", "chao", "cao" or "mahalanobis".
method	(Optional). A character string specifying ordination method. All methods available to the ordinate function of phyloseq are acceptable here as well ( Default is "PCOA"). "DCA", "CCA", "RDA", "CAP", "DPCoA", "NMDS", "MDS", "PCoA", "PCA", "Tsne".
grouping_column	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information. information.

Details

14/01/2020 ShenZhen China

Value

Returns a list of three items:

• A solution of the ordination

• A data.frame of betadispersion results; compared groups, corresponding pairwise observed p-values and significant labels.

• an object of class "adonis" with all components ; see adonis for details.

Author(s)

Hua Zou, Huahui Ren

References

http://userweb.eng.gla.ac.uk/umer.ijaz/, Umer Ijaz, 2015

Examples

data(physeq_data)
physeq <- physeq_data
ord.res <- ordination(physeq, method = "NMDS", grouping_column = "Stage")

rusher321/microbiotaPair documentation built on July 24, 2024, 8:40 p.m.