div_profile_plot {hilldiv}

Diversity profile plot

Description

Plot diversity profiles from objects generated with the function div_profile().

Usage

div_profile_plot(profile, colour, log, legend)

Arguments

profile

A div_profile() object or a vector/matrix containg diversity profile(s), with columns indicating samples/groups and rows indicating orders of diversity (q-values).

colour

A vector of RGB colours e.g. c("#34k235","#99cc00"). The number of vector items, must equal the number of samples or groups that are intended to plot.

log

Whether to transform Hill numbers to logarithmic scale (TRUE) or not (FALSE). This is useful when there are large differences between q values (e.g. sharp drop from q=0 to q=1), which might complicate visualization. Default: log=FALSE

legend

Whether to display the legend (TRUE) or not (FALSE) in diversity profiles containing multiple samples/groups. Default TRUE in multi-sample charts.

Details

Diversity profile plot

Value

A diversity profile plot.

Author(s)

Antton Alberdi, [e-mail]

References

Alberdi, A., Gilbert, M.T.P. (2019). A guide to the application of Hill numbers to DNA-based diversity analyses. Molecular Ecology Resources, 19, 804-817.

Chao, A., Chiu, C.H., & Jost, L. (2014). Unifying species diversity, phylogenetic diversity, functional diversity, and related similarity and differentiation measures through hill numbers. Annual Review of Ecology Evolution and Systematics, 45, 297-324.

See Also

div_profile, hill_div

Examples

data(bat.diet.otutable)
data(bat.diet.hierarchy)
#One sample example
bat.diet.sample <- bat.diet.otutable[,1]
profile.onesample <- div_profile(count=bat.diet.sample,qvalues=seq(from = 0, to = 5, by = (0.1)))
div_profile_plot(profile.onesample)
#Multiple samples
profile.multiplesamples <- div_profile(bat.diet.otutable)
div_profile_plot(profile.multiplesamples)
#Multiple groups (gamma diversity)
profile.multiplegroups <- div_profile(bat.diet.otutable,hierarchy=bat.diet.hierarchy,level="gamma")
div_profile_plot(profile.multiplegroups)