Score plot of multivariate analyses
Displays a score plot of a multivariate analysis.
MVA.scoreplot(x, xax = 1, yax = 2, scaling = 2, set = c(12, 1, 2), space = 1, byfac = TRUE, fac = NULL, barycenters = TRUE, stars = TRUE, contours = FALSE, dhist = TRUE, weights = 1, xlab = NULL, ylab = NULL, main = NULL, pch = 16, cex = 1, col = 1, points = TRUE, labels = NULL, main.pos = c("bottomleft", "topleft", "bottomright", "topright"), main.cex = 1.3, fac.lab = NULL, fac.cex = 1, legend = FALSE, legend.pos = c("topleft", "topright", "bottomleft", "bottomright"), legend.title = NULL, legend.lab = NULL, legend.cex = 1, drawextaxes = TRUE, drawintaxes = TRUE, xlim = NULL, ylim = NULL, keepmar = FALSE)
x: a multivariate analysis (see Details).xax: the horizontal axis.yax: the vertical axis. This can be set to NULL for a one-dimensional graph. The type of graph to be drawn in this case depends on the value of dhist.scaling: type of scaling. Only available with some analyses performed with the vegan package. See Details.set: scores to be displayed, when several sets are available (see Details). 12 (default) for both sets, 1 for rows or X, 2 for columns or Y.space: scores to be displayed, when several spaces are available (see Details). space is the number of the space to be plotted.byfac: only used with MCA and mix analyses (see Details). If TRUE, a separate score plot is displayed for each factor included in the analysis. In this case fac cannot be used and if main=NULL, the factor names are displayed as titles on the graphs.fac: an optional factor defining groups of individuals.barycenters: only used if fac is not NULL. If TRUE (default), the name of each group (defined by fac.lab) is diplayed at the position of the barycenter of this group. Available for two-dimensional graphs and for dotcharts in the one-dimensional case (see dhist).stars: only used if fac is not NULL. If TRUE (default), the individual of each group are linked to their corresponding barycenter.contours: only used if fac is not NULL. If TRUE, a polygon of contour is displayed for each group.dhist: only used in the one-dimensional case. If TRUE (default), a density histogram is displayed. If FALSE, a dotchart is displayed.weights: individual weights, used to calculate barycenter positions (see barycenters).xlab: legend of the horizontal axis. If NULL (default), automatic labels are used depending on the multivariate analysis.ylab: legend of the vertical axis. If NULL (default), automatic labels are used depending on the multivariate analysis. Available for two-dimensional graphs and for density histograms in the one-dimensional case (see dhist).main: optional title of the graph. Can be a vector of several values for MCA and mix analyses when byfac=TRUE (see byfac).pch: symbol(s) used for points, when points are displayed (see points). If fac is not NULL, can be a vector of length one or a vector giving one value per group. Otherwise a vector of any length can be defined, which is recycled if necessary. Available for two-dimensional graphs and for dotcharts in the one-dimensional case (see dhist). Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).cex: size of the points or of the labels (see points). Available for two-dimensional graphs and for dotcharts in the one-dimensional case (see dhist). For two-dimensional graphs: if fac is not NULL, can be a vector of length one or a vector giving one value per group; otherwise a vector of any length can be defined, which is recycled if necessary. For dotcharts, gives the size used for points and all labels (see dotchart). Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).col: color(s) used for points or labels (see points). If fac is not NULL, can be a vector of length one or a vector giving one value per group. Otherwise a vector of any length can be defined, which is recycled if necessary (not available for density histograms, see dhist). Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).points: only used for two-dimensional graphs. If FALSE, points are replaced with their corresponding label (defined by labels). Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).labels: used in two-dimensional graphs when points=FALSE and in dotcharts (see dhist). Names of the individuals. If NULL (default), labels correspond to row names of the data used in the multivariate analysis. Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).main.pos: position of the title, if main is not NULL. Default to "bottomleft". Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).main.cex: size of the title, if main is not NULL. Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).fac.lab: only used if fac is not NULL. Labels used to display barycenters in two-dimensional graphs or on the vertical axis of a dotchart in the one-dimensional case (see dhist). If NULL, levels of the factor defined by fac are used. In case of a MCA or a mix analysis with byfac=TRUE (see byfac), labels cannot be changed and correspond to the levels of the factor displayed on each graph.fac.cex: only used if fac is not NULL and in two-dimensional graphs. Labels used to display barycenters. Can be a vector of length one or a vector giving one value per group. Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).legend: logical indicating if a legend should be added to the graph. Available for two-dimensional graphs and for density histograms in the one-dimensional case (see dhist).legend.pos: position of the legend, if legend is TRUE. Default to "topleft".legend.title: optional title of the legend, if legend is TRUE. Not available for MCA and mix analyses when byfac=TRUE (see byfac).legend.lab: legend labels, if legend is TRUE. If NULL, labels defined by fac.labels are used (see fac.labels).legend.cex: size of legend labels, if legend is TRUE.drawextaxes: logical indicating if external axes should be drawn. Available for two-dimensional graphs and for density histograms in the one-dimensional case (see dhist).drawintaxes: logical indicating if internal axes should be drawn.xlim: limits of the horizontal axis. If NULL, limits are computed automatically. Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).ylim: only used in two-dimensional graphs. Limits of the vertical axis. If NULL, limits are computed automatically. Re-used for all graphs for MCA and mix analyses when byfac=TRUE (see byfac).keepmar: only used in two-dimensional graphs. Logical indicating if margins defined by MVA.scoreplot should be kept after plotting (necessary for biplots).This function should not be use directly. Prefer the general MVA.plot, to which all arguments can be passed.
Many multivariate analyses are supported, from various packages:
PCA: prcomp, princomp (if scores=TRUE), dudi.pca, rda, pca, pca. scaling can be defined for rda (see scores.rda).
sPCA: spca.
IPCA: ipca.
sIPCA: sipca.
PCoA: cmdscale (with at least on non-default argument), dudi.pco, wcmdscale (with at least one non-default argument), capscale, pco, pcoa.
nMDS: monoMDS, metaMDS, nmds, isoMDS.
LDA: lda, discrimin.
PLS-DA (PLS2 on a dummy-coded factor): plsda. X space only.
sPLS-DA (sPLS2 on a dummy-coded factor): splsda. X space only.
CPPLS: mvr. X space only.
PLSR: mvr, pls, plsR (plsRglm package). X space only.
sPLSR: pls. X space only.
PLS-GLR: plsRglm (plsRglm package).
PCR: mvr.
CDA: discrimin, discrimin.coa.
NSCOA: dudi.nsc.
MCA: dudi.acm.
Mix analysis: dudi.mix, dudi.hillsmith.
COA: dudi.coa, cca. Set 1 is rows, set 2 is columns. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set. scaling can be defined for cca (see scores.cca).
DCOA: dudi.dec. Set 1 is rows, set 2 is columns. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
PCIA: procuste. Set 1 is X, set 2 is Y. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
Procrustean superimposition: procrustes. Set 1 is X, set 2 is Y. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
GPA: GPA. Only the consensus ordination can be displayed.
DPCoA: dpcoa. Set 1 is categories, set 2 is collections. If set=12 (default), fac is not available and pch,cex, col can be defined differently for each set.
RDA (or PCAIV): pcaiv, pcaivortho, rda. With rda, space 1 is constrained space, space 2 is unconstrained space. Only constrained space is available with pcaiv, the opposite for pcaivortho. scaling can be defined for rda (see scores.rda).
db-RDA (or CAP): capscale, dbrda. Space 1 is constrained space, space 2 is unconstrained space.
CCA: pcaiv, cca. With rda, space 1 is constrained space, space 2 is unconstrained space. Only constrained space is available with pcaiv. Set 1 is rows, set 2 is columns. scaling can be defined for cca (see scores.cca).
CCorA: CCorA, rcc. Space 1 is X, space 2 is Y. With rcc a third space is available, in which coordinates are means of X and Y coordinates.
rCCorA: rcc. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
CIA: coinertia. Space 1 is X, space 2 is Y, space 3 is a "common" space where X and Y scores are normed. In space 3, set 1 is X and set 2 is Y. If set=12 in space 3 (default), fac is not available and pch,cex, col can be defined differently for each set.
2B-PLS: pls. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
2B-sPLS: pls. Space 1 is X, space 2 is Y, space 3 is a "common" space in which coordinates are means of X and Y coordinates.
rGCCA: rgcca, wrapper.rgcca. Space can be 1 to n, the number of blocks (i.e. datasets).
sGCCA: rgcca, wrapper.sgcca. Space can be 1 to n, the number of blocks (i.e. datasets).
DIABLO: block.plsda, block.splsda. Space can be 1 to n, the number of blocks (i.e. datasets).
Maxime HERVE maxime.herve@univ-rennes1.fr
data(iris) PCA <- prcomp(iris[,1:4]) MVA.plot(PCA,"scores") MVA.plot(PCA,"scores",fac=iris$Species,col=1:3,pch=15:17)
Useful links