plot_taxa: Local Contribution to Beta Diversity (LCBD)

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

Description

This function finds the most abundant taxa for each sample. It also calculates local contribution to beta diversity using a selected dissimilarity coefficient. It returns a ggplot object which a visual representation of the most abundant taxa for each of the samples. The number of top taxa can be suggested as an argument. The visual representation is limited to 21 top taxa, more information can be availed by supplying a file name to which details of LCBD can be written.

Usage

plot_taxa(physeq, grouping_column, method = "hellinger",
  number.taxa = 21, filename = NULL)

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.
method.	A method to used to calculate dissimilarity coefficents. Available methods are: "hellinger", "chord", "chisquare", "profiles", "percentdiff", "ruzicka", "divergence", "canberra", "whittaker", "wishart", "kulczynski", "jaccard", "sorensen", "ochiai", "ab.jaccard", "ab.sorensen", "ab.ochiai", "ab.simpson", "euclidean". the function uses "hellinger" as a default.
grouping_column(Required).	Name of a categorical variable that is preffered for grouping the. information.

Value

Returns a ggplot object. This can further be manipulated as preferred by user.

Author(s)

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

References

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

Examples

plot_taxa(physeq, "Country")

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