plot_anova_env: ANOVA of environmental variables

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

Description

This functions applies analysis of variance on the measured environmental variables in specified groups and constructs a plot showing how the environmental variables vary in the groups. The plot is annotated with significance level as obtained from anova.

Usage

plot_anova_env(physeq, grouping_column, pValueCutoff = 0.05,
  select.variables = 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.
grouping_column	(Required). Name of a categorical variable that is preffered for grouping the. information, this should be one of the components of grouping vector.
pValueCutoff.	p-value threshold for significance of anova results, default set to 0.05.
select.variables.	A vector of character strings(s) specifying environmental variable(s) to be analysed. If not supplied, all numeric variables are analysed.

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

data(pitlatrine)
physeq<-pitlatrine
p1<-plot_anova_env(physeq,grouping_column =  "Country",select.variables=c("Temp","pH"))
print(p1)

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