plot_anova_diversity: Alpha diversity with ANOVA

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

Description

This function calculates alpha diversity of provided community data using selected indices/method(s). It performs pair-wise ANOVA of diversity measures between groups and outputs a plot for each of the selected methods(indices) annotated with significance levels.

Usage

plot_anova_diversity(physeq, method, grouping_column,
  pValueCutoff = 0.05, outfile = "anova_diversity.csv")

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.
method	(Required). A list of character strings specifying method to be used to calculate for alpha diversity in the data. Available methods are: "richness", "fisher", "simpson", "shannon" and "evenness".
grouping_column	(Required). A character string specifying the name of a categorical variable containing grouping information.

Value

Returns a ggplot object which can further be manipulated further.

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
p<-plot_anova_diversity(physeq, method = c("richness","simpson"),grouping_column =  "Country",pValueCutoff=0.05)
plot_anova_diversity(physeq, method = c("richness","shannon"), grouping_column = "Depth")
print(p)

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