generateFSO: Fuzzy Set Ordination

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

Description

This function uses fuzzy set ordination to test effects of pertubation in environmental variables to community structure. It returns an ordination plot which is annotated with a correlation between the original values of the variable and the fuzzy values together with corresponding significance label.

Usage

generateFSO(physeq, grouping_column, method = 1, indices = NULL,
  filename = NULL, type = 1, step_across = F)

Arguments

grouping_column	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information. information.
method	An integer specifying method for computing similarity indices, 1 = Baroni-Urbani & Buser, 2 = Horn and 3 = Yule .
type	(optional) An integer (1 or 2), for fso or mfso respectively.
step_across	(optional) logical variable setting it to TRUE is for step-across correction which might improve the ordination
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.

Value

A ggplot object of fuzzy set against original values which is annotated with a correlation between them and a significance label.

Author(s)

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

References

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

http://www.nku.edu/~boycer/fso/

Examples

data(pitlatrine)
physeq <- taxa_level(pitlatrine, "Phylum")
p <- generateFSO(physeq, grouping_column="Country", method=1, type=1)
print(p)

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