spca {adegenet} | R Documentation |
These functions are designed to perform a spatial principal
component analysis and to display the results. They call upon
multispati
from the ade4
package.
spca
performs the spatial component analysis. Other
functions are:
- print.spca
: prints the spca content
- summary.spca
: gives variance and autocorrelation
statistics
- plot.spca
: usefull graphics (connection network, 3 different
representations of map of scores, eigenvalues barplot and
decomposition)
- screeplot.spca
: decomposes spca eigenvalues into variance and
autocorrelation
- colorplot.spca
: represents principal components of sPCA in
space using the RGB system.
A tutorial describes how to perform a sPCA: see
http://adegenet.r-forge.r-project.org/files/tutorial-spca.pdf or
type adegenetTutorial(which="spca")
.
spca(obj, xy=NULL, cn=NULL, matWeight=NULL, scale=FALSE, scale.method=c("sigma","binom"), scannf=TRUE, nfposi=1, nfnega=1, type=NULL, ask=TRUE, plot.nb=TRUE, edit.nb=FALSE, truenames=TRUE, d1=NULL, d2=NULL, k=NULL, a=NULL, dmin=NULL) ## S3 method for class 'spca': print(x, ...) ## S3 method for class 'spca': summary(object, ..., printres=TRUE) ## S3 method for class 'spca': plot(x, axis = 1, useLag=FALSE, ...) ## S3 method for class 'spca': screeplot(x, ..., main=NULL) ## S3 method for class 'spca': colorplot(x, axes=1:ncol(x$li), useLag=FALSE, ...)
obj |
a genind or genpop object. |
xy |
a matrix or data.frame with two columns for x and y
coordinates. Seeked from obj$other$xy if it exists when xy is not
provided. Can be NULL if a nb object is provided in
cn .Longitude/latitude coordinates should be converted first by a given projection (see See Also section). |
cn |
a connection network of the class 'nb' (package spdep). Can be NULL if xy is provided. Can be easily obtained using the function chooseCN (see details). |
matWeight |
a square matrix of spatial weights, indicating the
spatial proximities between entities. If provided, this argument
prevails over cn (see details). |
scale |
a logical indicating whether alleles should be scaled to unit variance (TRUE) or not (FALSE, default). |
scale.method |
a character string indicating the method used for
scaling allele frequencies. This argument is passed to
scaleGen function (see ?scaleGen ). |
scannf |
a logical stating whether eigenvalues should be chosen interactively (TRUE, default) or not (FALSE). |
nfposi |
an integer giving the number of positive eigenvalues retained ('global structures'). |
nfnega |
an integer giving the number of negative eigenvalues retained ('local structures'). |
type |
an integer giving the type of graph (see details in
chooseCN help page). If provided, ask is set to FALSE. |
ask |
a logical stating whether graph should be chosen interactively (TRUE,default) or not (FALSE). |
plot.nb |
a logical stating whether the resulting graph should be plotted (TRUE, default) or not (FALSE). |
edit.nb |
a logical stating whether the resulting graph should be edited manually for corrections (TRUE) or not (FALSE, default). |
truenames |
a logical stating whether true names should be used for 'obj' (TRUE, default) instead of generic labels (FALSE) |
d1 |
the minimum distance between any two neighbours. Used if
type=5. |
d2 |
the maximum distance between any two neighbours. Used if
type=5 . |
k |
the number of neighbours per point. Used if
type=6 . |
a |
the exponent of the inverse distance matrix. Used if
type=7 . |
dmin |
the minimum distance between any two distinct points. Used
to avoid infinite spatial proximities (defined as the inversed
spatial distances). Used if type=7 . |
x |
a spca object. |
object |
a spca object. |
printres |
a logical stating whether results should be printed on the screen (TRUE, default) or not (FALSE). |
axis |
an integer between 1 and (nfposi+nfnega) indicating which axis should be plotted. |
main |
a title for the screeplot; if NULL, a default one is used. |
... |
further arguments passed to other methods. |
axes |
the index of the columns of X to be represented. Up to three axes can be chosen. |
useLag |
a logical stating whether the lagged components
(x\$ls ) should be used instead of the components (x\$li ). |
The spatial principal component analysis (sPCA) is designed to
investigate spatial patterns in the genetic variability. Given
multilocus genotypes (individual level) or allelic frequency
(population level) and spatial coordinates, it finds individuals (or
population) scores maximizing the product of variance and spatial
autocorrelation (Moran's I). Large positive and negative eigenvalues
correspond to global and local structures.
Spatial weights can be obtained in several ways, depending how the
arguments xy
, cn
, and matWeight
are set.
When several acceptable ways are used at the same time, priority is as
follows:
matWeight
> cn
> xy
The class spca
are given to lists with the following
components:
eig |
a numeric vector of eigenvalues. |
nfposi |
an integer giving the number of global structures retained. |
nfnega |
an integer giving the number of local structures retained. |
c1 |
a data.frame of alleles loadings for each axis. |
li |
a data.frame of row (individuals or populations) coordinates onto the sPCA axes. |
ls |
a data.frame of lag vectors of the row coordinates; useful to clarify maps of global scores . |
as |
a data.frame giving the coordinates of the PCA axes onto the sPCA axes. |
call |
the matched call. |
xy |
a matrix of spatial coordinates. |
lw |
a list of spatial weights of class listw . |
Other functions have different outputs:
- summary.spca
returns a list with 3 components: Istat
giving the null, minimum and maximum Moran's I values; pca
gives variance and I statistics for the principal component analysis;
spca
gives variance and I statistics for the sPCA.
- plot.spca
returns the matched call.
- screeplot.spca
returns the matched call.
Thibaut Jombart jombart@biomserv.univ-lyon1.fr
Jombart, T., Devillard, S., Dufour, A.-B. and Pontier, D. Revealing cryptic spatial patterns in genetic variability by a new multivariate method. Heredity, 101, 92–103.
Wartenberg, D. E. (1985) Multivariate spatial correlation: a method for exploratory geographical analysis. Geographical Analysis, 17, 263–283.
Moran, P.A.P. (1948) The interpretation of statistical maps. Journal of the Royal Statistical Society, B 10, 243–251.
Moran, P.A.P. (1950) Notes on continuous stochastic phenomena. Biometrika, 37, 17–23.
de Jong, P. and Sprenger, C. and van Veen, F. (1984) On extreme values of Moran's I and Geary's c. Geographical Analysis, 16, 17–24.
spcaIllus
, a set of simulated data illustrating
the sPCA
global.rtest
and local.rtest
chooseCN
, multispati
,
multispati.randtest
convUL
to convert longitude/latitude to
UTM coordinates.
## data(spcaIllus) illustrates the sPCA ## see ?spcaIllus ## example(spcaIllus)