plot_ordination: Ordination plots

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

Ordination plots

Description

This function produces visualisation of ordination and beta dispersion results.

Usage

plot_ordination(physeq, method, grouping_column)

Arguments

ordination.res	(Required). A solution of ordination results returned from ordination.
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.
PID	id (Required) for paired test
paired
circle
time_colour	a vector include the color

Details

14/01/2020 ShenZhen China

Value

Returns a ggplot object.

Author(s)

Hua Zou; hua huiren

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")
plot_ordination(ord.res, method = "PCoA", grouping_column = "Stage", PID = "ID")

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