trueDiversity: True diversity of sequences
In bcRep: Advanced Analysis of B Cell Receptor Repertoire Data

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

This function provides information about the true diversity. Richness or diversity is calculated for sequences of the same length, for each position. Analysis of true diversity of order 0 (richness), 1 (Shannon) and 2 (Simpson) is possible (see Details).

trueDiversity returns a list containing diversity indices.

plotTrueDiversity gives an overview about the richness or diversity of sequences with the same length.

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trueDiversity(sequences = NULL, aaDistribution.tab = NULL, order = c(0,1,2))

plotTrueDiversity(trueDiversity.tab=NULL, mean.plot=T, color="black", PDF=NULL)

`sequences`	Vector containing sequences (see Details)
`aaDistribution.tab`	Output of the function `AADistribution()` (see Details)
`order`	True diversity order (q). Values: 0, 1, 2 (default: 1)
`trueDiversity.tab`	Output of function `trueDiversity()`
`mean.plot`	Includes only one figure with mean diversities (default = T)
`color`	color used for plot (default: black)
`PDF`	PDF project name (see Details)

This functions needs either a vector of sequences or the output of AADistribution() as input. In first case AADistribution() is applied to data set and than diversity is measured. 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.

plotTrueDiversity 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).

The PDF character string should be only the project name (without ".pdf"). A figure called "PDF"_True-diversity_q"order".pdf will be saved to the working directory.

Output is a list containing

`True_diversity_order`	order of true diversity (q=0,1,2)
`True_diversity`	a list of true diversities for each position of each length

For large datasets computational time can be extensive for the calculation of amino acid proportions.

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

aaDistribution, trueDiversity, diversity

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data(aaseqtab)
trueDiv<-trueDiversity(sequences = aaseqtab$CDR3_IMGT, order = 1)
## Not run: plotTrueDiversity(trueDiversity.tab=trueDiv,color="red", PDF="Example")