scoreplot {pls}R Documentation

Plots of Scores, Loadings and Correlation Loadings

Description

Functions to make scatter plots of scores or correlation loadings, and scatter or line plots of loadings.

Usage

scoreplot(object, comps = 1:2, labels, identify = FALSE, type = "p",
          xlab, ylab, ...)
## S3 method for class 'scores':
plot(x, ...)

loadingplot(object, comps = 1:2, scatter = FALSE, labels, identify = FALSE,
            type, lty, lwd = NULL, pch, cex = NULL, col, legendpos,
            xlab, ylab, ...)
## S3 method for class 'loadings':
plot(x, ...)

corrplot(object, comps = 1:2, labels, identify = FALSE, type = "p",
          xlab, ylab, ...)

Arguments

object an mvr object. The fitted model.
comps integer vector. The components to plot.
scatter logical. Whether the loadings should be plotted as a scatter instead of as lines.
labels optional. Labels to use instead of plotting symbols. If scatter = FALSE in loadingplot, they are used to label the x axis tick marks. Either a vector (of length > 1) of labels, or one of "names" and "numbers" for using row names and row numbers, respectively.
identify logical. Whether to use identify to interactively identify points. See below.
type character. What type of plot to make. Defaults to "p" (points) for scatter plots and "l" (lines) for line plots. See plot for a complete list of types (not all types are possible/meaningful for all plots).
lty vector of line types (recycled as neccessary). Line types can be specified as integers or character strings (see par for the details).
lwd vector of positive numbers (recycled as neccessary), giving the width of the lines.
pch plot character. A character string or a vector of single characters or integers (recycled as neccessary). See points for all alternatives.
cex numeric vector of character expansion sizes (recycled as neccessary) for the plotted symbols.
col character or integer vector of colors for plotted lines and symbols (recycled as neccessary). See par for the details.
legendpos Legend position. Optional. Ignored if scatter is TRUE. If present, a legend is drawn at the given position. The position can be specified symbolically (e.g., legendpos = "topright"). This requires R >= 2.1.0. Alternatively, the position can be specified explicitly (legendpos = t(c(x,y))) or interactively (legendpos = locator()).
xlab,ylab titles for x and y axes. Typically character strings, but can be expressions or lists. See title for details.
x a scores or loadings object. The scores or loadings to plot.
... further arguments sent to the underlying plot function(s).

Details

plot.scores is simply a wrapper calling scoreplot, passing all arguments. Similarly for plot.loadings.

scoreplot makes one or more scatter plots of the scores, depending on how many components are selected. If one or two components are selected, and identify is TRUE, the function identify is used to interactively identify points.

If scatter is TRUE, loadingplot works exactly like scoreplot. Otherwise, it makes a lineplot of the selected loading vectors, and if identify is TRUE, uses identify to interactively identify points. Also, if legendpos is given, a legend is drawn at the position indicated.

corrplot works exactly like scoreplot, except that at least two components must be selected. The “correlation loadings”, i.e. the correlations between each variable and the selected components, are plotted as pairwise scatter plots, with two concentric circles of radius 0.5 and 1.

scoreplot, loadingplot and corrplot can also be called through the plot method for mvr objects, by specifying plottype as "scores", "loadings" or "correlation", respectively. See plot.mvr.

scoreplot and loadingplot also work with princomp objects. (However, plot(scores(...)) and plot(loadings(...)) will not work.)

Value

The functions return whatever the underlying plot function (or identify) returns.

Note

legend has many options. If you want greater control over the appearance of the legend, omit the legendpos argument and call legend manually.

Graphical parametres (such as pch and cex) can also be used with scoreplot and corrplot. They are not listed in the argument list simply because they are not handled specifically in the function (unlike in loadingplot), but passed directly to the underlying plot functions by ....

Author(s)

Ron Wehrens and Bjørn-Helge Mevik

See Also

mvr, plot.mvr, scores, loadings, identify, legend

Examples

data(NIR)
mod <- plsr(y ~ X, ncomp = 10, data = NIR)
## These three are equivalent:
## Not run: 
scoreplot(mod, comps = 1:5)
plot(scores(mod), comps = 1:5)
plot(mod, plottype = "scores", comps = 1:5)

loadingplot(mod, comps = 1:5)
loadingplot(mod, comps = 1:5, legendpos = "topright") # With legend
loadingplot(mod, comps = 1:5, scatter = TRUE) # Plot as scatterplots

corrplot(mod, comps = 1:2)
corrplot(mod, comps = 1:3)
## End(Not run)

[Package pls version 1.1-0 Index]