compare.trueDiversity: Compare richness or diversity of different samples
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

Description Usage Arguments Details Value Note Author(s) References See Also Examples

This function compares the richness or diversity of different samples. Analysis can be done for order 0 (richness), 1 (Shannon) and 2 (Simpson) (see Details). Parallel processing is possible.

compare.trueDiversity(sequence.list = NULL, comp.aaDistribution.tab = NULL, 
     order = c(0, 1, 2), names = NULL, nrCores = 1)

plotCompareTrueDiversity(comp.tab = NULL, mean.plot=T, colors = NULL, 
    title = NULL, PDF = NULL)

`sequence.list`	A list containing vectors of amino acid sequences of each sample (see Details)
`comp.aaDistribution.tab`	Output from `compare.aaDistribution()` (see Details)
`order`	True diversity order (q). Values: 0, 1, 2
`names`	A vector containing names for the samples (default: like Sample1, Sample2, ...)
`nrCores`	Number of cores used for parallel processing
`comp.tab`	Output tab from `compare.trueDiversity()`
`mean.plot`	Includes only one figure with mean diversities (default = T)
`colors`	Colors used for individuals (default: rainbow)
`title`	Title of plot
`PDF`	PDF project name (see Details)

This functions needs either a list containing vectors of sequences or the output of

compare.aaDistribution() as input. In first case compare.aaDistribution() is first applied to data set. Richness or diversity is calculated for sequences of the same length, for each position. Analysis of true diversity of order 0, 1 and 2 is possible. Order 0: Richness (in this case it represents number of different amino acids per position). Order 1: Exponential function of Shannon entropy using the natural logarithm (weights all amino acids by their frequency). Order 2: Inverse Simpson entropy (weights all amino acids by their frequency, but weights are given more to abundant amino acids). These indices are very similar (Hill, 1973). For example the exponential function of Shannon index is linearly related to inverse Simpson.

plotCompareTrueDiversity returns an image with diversity plots for each length, if mean.plot = F. In the case of mean.plot = T, only one figure is returned, where mean diversity values for each sequence length are plotted. Each plot contains the richness or diversity (y-axis) for each position (x-axis). Individuals are color coded.

The PDF character string should be only the project name (without ".pdf").

A figure called "PDF"_Comparison_True-diversity_q"order".pdf will be saved to the working directory.

Output is a list containing 1) the diversity order, and 2) diversity values for each individual and each sequence length.

For large datasets computational time can be extensive.

Julia Bischof

M. O. Hill: Diversity and Evenness: A Unifying Notation and Its Consequences; Ecology 54:2, p 427-432 (1973)

Lou Jost: Entropy and diversity; OIKOS 113:2 (2006)

Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre, Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos, M. Henry H. Stevens and Helene Wagner (2015). vegan: Community Ecology Package. R package version 2.3-0. http://CRAN.R-project.org/package=vegan

compare.trueDiversity, plotCompareTrueDiversity, trueDiversity, compare.aaDistribution

data(aaseqtab)
data(aaseqtab2)

trueDiv.comp<-compare.trueDiversity(sequence.list = list(aaseqtab$CDR3_IMGT, 
     aaseqtab2$CDR3_IMGT), names = c("IndA", "IndB"), order = 1, nrCores = 1)
## Not run: 
plotCompareTrueDiversity(comp.tab = trueDiv.comp, PDF = "Example")

## End(Not run)