plot_cca: Canonical Correspondence Analysis plot

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

Description

This function finds a set of best environmental variables that describe community structure superimposes them on the ordination plot.

Usage

plot_cca(physeq, grouping_column, pvalueCutoff = 0.01,
  norm_method = NULL, env.variables = NULL, num.env.variables = NULL,
  exclude.variables = NULL, draw_species = F)

Arguments

'physeq'	is a required phyloseq object containing taxa abundance and meta data.
'grouping_column'	is the variable in the meta data with respect to which the data should be grouped,
'pvalueCutoff'	the threshold p-value in 'anova' of distance matrices, default set to '0.05'.
'env.variables'	is a list of variables prefered to be on the cca plot.
'exclude.variables'	a list of variables to be excluded from the cca plot.
'num.env.variables'	is an integer specifying the number of variables to show on the cca plot.

Value

A ggplot object

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(pitlatrine)
physeq<-data(physeq)
ccaplot  <- plot_cca(physeq, grouping_column = "Country")

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