plot_cca: Canonical Correspondence Analysis plot

Description Usage Arguments Value Author(s) References Examples

Description

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

Usage

1
2
3
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 assekagiri@gmail.com, Umer Zeeshan Ijaz Umer.Ijaz@glasgow.ac.uk

References

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

Examples

1
2
3
data(pitlatrine)
physeq<-data(physeq)
ccaplot  <- plot_cca(physeq, grouping_column = "Country")

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