bcRep (version 1.3.6)

trueDiversity: True diversity of sequences

Description

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.

Usage

trueDiversity(sequences = NULL, aaDistribution.tab = NULL, order = c(0,1,2))
plotTrueDiversity(trueDiversity.tab=NULL, mean.plot=T, color="black", PDF=NULL)

Arguments

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)

Value

Output is a list containing

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.

References

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

See Also

aaDistribution, trueDiversity, diversity

Examples

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