MVA.loadplot: Loading plot of multivariate analyses

In RVAideMemoire: Testing and Plotting Procedures for Biostatistics

Loading plot of multivariate analyses

Description

Displays a loading plot of a multivariate analysis.

Usage

MVA.loadplot(x, xax = 1, yax = 2, fac = NULL, set = c(12, 1, 2), space = 1, map = TRUE,
  xlab = NULL, ylab = NULL, main = NULL, points = TRUE, ident = TRUE, links = TRUE, 
  line = TRUE, labels = NULL, main.pos = c("bottomleft", "topleft","bottomright",
  "topright"), main.cex = 1.3, legend = FALSE, legend.pos = c("topleft", "topright",
  "bottomleft", "bottomright"), legend.title = NULL, legend.lab = NULL, pch = 16,
  cex = 1, col = 1, lwd = 1, lty = 1, drawextaxes = TRUE, drawintaxes = TRUE, xlim = NULL,
  ylim = NULL)

Arguments

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.
fac	only used for one-dimensional graphs. An optional factor defining groups of variables.
set	variables to be displayed, when several sets are available (see Details). 12 (default) for both sets, 1 for X, 2 for Y.
space	variables to be displayed, when several spaces are available (see Details). space is the number of the space to be plotted.
map	logical indicating if a two-dimensional (TRUE, default) or a one-dimensional graph should be drawn. A one-dimensional graph can show loadings for one or two dimensions, both horizontally.
xlab	only used for two-dimensional graphs. 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.
main	optional title of the graph.
points	only used for two-dimensional graphs. If FALSE, lines or points (see links) are replaced with their corresponding label (defined by labels).
ident	logical indicating if variable names should be displayed. Only used when points=TRUE for two-dimensional graphs.
links	only used for two-dimensional graphs when points=TRUE. Logical indicating if variables should be linked to the origin of the graph. If FALSE, points are displayed at the extremity of the segments.
line	only used for one-dimensional graphs when yax=NULL. Logical indicating if loadings should be linked (default) as displayed as sticks.
labels	only used if ident=TRUE. Names of the variables. If NULL (default), labels correspond to variable names found in the data used in the multivariate analysis.
main.pos	only used for one-dimensional graphs. Position of the title, if main is not NULL. Default to "bottomleft".
main.cex	size of the title, if main is not NULL.
legend	logical indicating if a legend should be added to the graph.
legend.pos	position of the legend, if legend is TRUE. Default to "topleft".
legend.title	optional title of the legend, if legend is TRUE.
legend.lab	legend labels, if legend is TRUE. If NULL for a one-dimensional graph, dimension names are used. If NULL for a two-dimensional graph, levels of the factor defined by fac are used.
pch	only used for two-dimensional graphs. Symbol(s) used for points, when points are displayed (see links). 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.
cex	size of the points and/or of the variable names. 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.
col	color(s) used for points, variable names and/or lines/sticks. For one-dimensional graphs, can be a vector of length one or a vector giving one value per line. 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 (not available for density histograms, see dhist).
lwd	width of lines. For one-dimensional graphs, can be a vector of length one or a vector giving one value per line. 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.
lty	only used for one-dimensional graphs. Can be a vector of length one or a vector giving one value per line.
drawextaxes	logical indicating if external axes should be drawn.
drawintaxes	only used for two-dimensional graphs. Logical indicating if internal axes should be drawn.
xlim	only used in two-dimensional graphs. Limits of the horizontal axis. If NULL, limits are computed automatically.
ylim	limits of the vertical axis. If NULL, limits are computed automatically.

Details

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, dudi.pca, rda, pca, pca.

- sPCA: spca.

- IPCA: ipca.

- sIPCA: sipca.

- 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.

- PCIA: procuste. Set 1 is X, set 2 is Y.

- 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.

- CCorA: rcc. Space 1 is X, space 2 is Y.

- rCCorA: rcc. Space 1 is X, space 2 is Y.

- CIA: coinertia. Space 1 is X, space 2 is Y.

- 2B-PLS: pls. Space 1 is X, space 2 is Y.

- 2B-sPLS: pls. Space 1 is X, space 2 is Y.

- rGCCA: wrapper.rgcca. Space can be 1 to n, the number of blocks (i.e. datasets).

- sGCCA: 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).

Author(s)

Maxime HERVE <[e-mail]>

Examples

require(ade4)
data(olympic)
PCA <- dudi.pca(olympic$tab,scannf=FALSE)
MVA.plot(PCA,"load")

RVAideMemoire documentation built on Nov. 6, 2023, 5:07 p.m.