plot.ordination: Ordination plots
In umerijaz/microbiomeSeq: Microbial community analysis in an environmental context.

This function produces visualisation of ordination and beta dispersion results.

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## S3 method for class 'ordination'
plot(ordination.res, method, pvalue.cutoff = 0.05,
  show.pvalues = T, N = 5, extra_marginspace = 0.35)

`ordination.res`	A solution of ordination results returned from 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.
`meta_table:`	A `data.frame` of environmental variables bearing atleast the grouping variable.
`method:`	A character string specifying ordination method used to generate the ordination to plot.
`grouping_column`	(Required). Character string specifying name of a categorical variable that is preffered for grouping the information.
`adn_res:`	`adonis` results to be annotated on the plot.
`betadisper_res:`	`data.frame` of betadispersion results to be annotated on the ordination plot.
`pvalue.cutoff:`	pvalue threshold for significant dispersion results.
`show.pvalues:`	A logical value specifying whether to annotate p-values or only significant labels for dispersion results.
`N:`	Integer specifying number of group pairs to show on plot.
`extra_marginspace:`	units to add extra space in margins to accomodate off plot area annotations.

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

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

umerijaz/microbiomeSeq index

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