mdpcoa: Multiple Double Principal Coordinate Analysis

In ade4: Analysis of Ecological Data: Exploratory and Euclidean Methods in Environmental Sciences

Multiple Double Principal Coordinate Analysis

Description

The DPCoA analysis (see dpcoa) has been developed by Pavoine et al. (2004). It has been used in genetics for describing inter-population nucleotide diversity. However, this procedure can only be used with one locus. In order to measure and describe nucleotide diversity with more than one locus, we developed three versions of multiple DPCoA by using three ordination methods: multiple co-inertia analysis, STATIS, and multiple factorial analysis. The multiple DPCoA allows the impact of various loci in the measurement and description of diversity to be quantified and described. This method is general enough to handle a large variety of data sets. It complements existing methods such as the analysis of molecular variance or other analyses based on linkage disequilibrium measures, and is very useful to study the impact of various loci on the measurement of diversity.

Usage

mdpcoa(msamples, mdistances = NULL, method = 
    c("mcoa", "statis", "mfa"), 
    option = c("inertia", "lambda1", "uniform", "internal"), 
    scannf = TRUE, nf = 3, full = TRUE, 
    nfsep = NULL, tol = 1e-07)
kplotX.mdpcoa(object, xax = 1, yax = 2, mfrow = NULL, 
    which.tab = 1:length(object$nX), includepop = FALSE, 
    clab = 0.7, cpoi = 0.7, unique.scale = FALSE, 
    csub = 2, possub = "bottomright")
prep.mdpcoa(dnaobj, pop, model, ...)

Arguments

msamples	A list of data frames with the populations as columns, alleles as rows and abundances as entries. All the tables should have equal numbers of columns (populations). Each table corresponds to a locus;
mdistances	A list of objects of class 'dist', corresponding to the distances among alleles. The order of the loci should be the same in msamples as in mdistances;
method	One of the three possibilities: "mcoa", "statis", or "mfa". If a vector is given, only its first value is considered;
option	One of the four possibilities for normalizing the population coordinates over the loci: "inertia", "lambda1", "uniform", or "internal". These options are used with MCoA and MFA only;
scannf	a logical value indicating whether the eigenvalues bar plots should be displayed;
nf	if scannf is FALSE, an integer indicating the number of kept axes for the multiple analysis;
full	a logical value indicating whether all the axes should be kept in the separated analyses (one analysis, DPCoA, per locus);
nfsep	if full is FALSE, a vector indicating the number of kept axes for each of the separated analyses;
tol	a tolerance threshold for null eigenvalues (a value less than tol times the first one is considered as null);
object	an object of class 'mdpcoa';
xax	the number of the x-axis;
yax	the number of the y-axis;
mfrow	a vector of the form 'c(nr,nc)', otherwise computed by as special own function 'n2mfrow';
which.tab	a numeric vector containing the numbers of the loci to analyse;
includepop	a logical indicating if the populations must be displayed. In that case, the alleles are displayed by points and the populations by labels;
clab	a character size for the labels;
cpoi	a character size for plotting the points, used with 'par("cex")'*cpoint. If zero, no points are drawn;
unique.scale	if TRUE, all the arrays of figures have the same scale;
csub	a character size for the labels of the arrays of figures used with 'par("cex")*csub';
possub	a string of characters indicating the sub-title position ("topleft", "topright", "bottomleft", "bottomright");
dnaobj	a list of dna sequences that can be obtained with the function read.dna of the ape package;
pop	a factor that gives the name of the population to which each sequence belongs;
model	a vector giving the model to be applied for the calculations of the distances for each locus. One model should be attributed to each locus, given that the loci are in alphabetical order. The models can take the following values: "raw", "JC69", "K80" (the default), "F81", "K81", "F84", "BH87", "T92", "TN93", "GG95", "logdet", or "paralin". See the help documentation for the function "dist.dna" of ape for a describtion of the models.
...	... further arguments passed to or from other methods

Details

An object obtained by the function mdpcoa has two classes. The first one is "mdpcoa" and the second is either "mcoa", or "statis", or "mfa", depending on the method chosen. Consequently, other functions already available in ade4 for displaying graphical results can be used: With MCoA, - plot.mcoa: this function displays (1) the differences among the populations according to each locus and the compromise, (2) the projection of the principal axes of the individual analyses onto the synthetic variables, (3) the projection of the principal axes of the individual analyses onto the co-inertia axes, (4) the squared vectorial covariance among the coinertia scores and the synthetic variables; - kplot.mcoa: this function divides previous displays (figures 1, 2, or 3 described in plot.mcoa) by giving one plot per locus.

With STATIS, - plot.statis: this function displays (1) the scores of each locus according to the two first eigenvectors of the matrix Rv, (2) the scatter diagram of the differences among populations according to the compromise, (3) the weight attributed to each locus in abscissa and the vectorial covariance among each individual analysis with the notations in the main text of the paper) and the compromise analysis in ordinates, (4) the covariance between the principal component inertia axes of each locus and the axes of the compromise space; - kplot.statis: this function displays for each locus the projection of the principal axes onto the compromise space.

With MFA, - plot.mfa: this function displays (1) the differences among the populations according to each locus and the compromise, (2) the projection of the principal axes of the individual analyses onto the compromise, (3) the covariance between the principal component inertia axes of each locus and the axes of the compromise space, (4) for each axis of the compromise, the amount of inertia conserved by the projection of the individual analyses onto the common space. - kplot.mfa: this function displays for each locus the projection of the principal axes and populations onto the compromise space.

Value

The functions provide the following results:

dist.ktab

returns an object of class dist;

Author(s)

Sandrine Pavoine [e-mail]

References

Pavoine, S. and Bailly, X. (2007) New analysis for consistency among markers in the study of genetic diversity: development and application to the description of bacterial diversity. BMC Evolutionary Biology, 7, e156.

Pavoine, S., Dufour, A.B. and Chessel, D. (2004) From dissimilarities among species to dissimilarities among communities: a double principal coordinate analysis. Journal of Theoretical Biology, 228, 523–537.

See Also

dpcoa

Examples

# The functions used below require the package ape
data(rhizobium)
if (requireNamespace("ape", quietly = TRUE)) {
dat <- prep.mdpcoa(rhizobium[[1]], rhizobium[[2]], 
    model = c("F84", "F84", "F84", "F81"), pairwise.deletion = TRUE)
sam <- dat$sam
dis <- dat$dis
# The distances should be Euclidean. 
# Several transformations exist to render a distance object Euclidean 
# (see functions cailliez, lingoes and quasieuclid in the ade4 package). 
# Here we use the quasieuclid function.
dis <- lapply(dis, quasieuclid)
mdpcoa1 <- mdpcoa(sam, dis, scannf = FALSE, nf = 2)

# Reference analysis
plot(mdpcoa1)

# Differences between the loci
kplot(mdpcoa1)

# Alleles projected on the population maps.
kplotX.mdpcoa(mdpcoa1)
}

ade4 documentation built on Feb. 16, 2023, 7:58 p.m.