ordination: Ordination and beta dispersion

In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

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, which_distance = "bray", method, grouping_column,
  pvalue.cutoff = 0.05)

Arguments

grouping_column	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information. information.
pvalue.cutoff	pvalue threshold for significant dispersion results.
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.
method.	A character string specifying ordination method. All methods available to the ordinate function of phyloseq are acceptable here as well.
which_distance.	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".

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)

Alfred Ssekagiri [e-mail], Umer Zeeshan Ijaz [e-mail]

References

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

Examples

data(pitlatine)
physeq <- pitlatrine
ord.res <- ordination(physeq, method="NMDS", grouping_column="Depth")

umerijaz/microbiomeSeq documentation built on May 30, 2019, 3:13 p.m.