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

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

    corrplot(object, comps = 1:2, labels, plotx = TRUE, ploty = FALSE,
             radii = c(sqrt(1/2), 1), identify = FALSE, type = "p",
             xlab, ylab, col, ...)

### Arguments

`object` | an R 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. Alternative plot labels or x axis labels. See Details.
`plotx` | locical. Whether to plot the X correlation loadings. Defaults to `TRUE`.
`ploty` | locical. Whether to plot the Y correlation loadings. Defaults to `FALSE`.
`radii` | numeric vector, giving the radii of the circles drawn in `corrplot`. The default radii represent 50% and 100% explained variance of the X variables by the chosen components.
`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.
`pretty.xlabels` | logical. If `TRUE`, `loadingplot` tries to plot the x labels more nicely. See Details.
`xlim` | optional vector of length two, with the x limits of the plot.
`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` is generic, currently with a default method that works for matrices and any object for which `scores` returns a matrix. The default `scoreplot` method 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.

Also `loadingplot` is generic, with a default method that works for matrices and any object where `loadings` returns a matrix. If `scatter` is `TRUE`, the default method works exactly like the default `scoreplot` method. 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 the default `scoreplot` method, except that at least two components must be selected. The “correlation loadings”, i.e. the correlations between each variable and the selected components (see References), are plotted as pairwise scatter plots, with concentric circles of radii given by `radii`. Each point corresponds to a variable. The squared distance between the point and origin equals the fraction of the variance of the variable explained by the components in the panel. The default `radii` corresponds to 50% and 100% explained variance. By default, only the correlation loadings of the X variables are plotted, but if `ploty` is `TRUE`, also the Y correlation loadings are plotted.

`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`.

The argument `labels` can be a vector of labels or one of `"names"` and `"numbers"`.

If a scatter plot is produced (i.e., `scoreplot`, `corrplot`, or `loadingplot` with `scatter = TRUE`), the labels are used instead of plot symbols for the points plotted. If `labels` is `"names"` or `"numbers"`, the row names or row numbers of the matrix (scores, loadings or correlation loadings) are used.

If a line plot is produced (i.e., `loadingplot`), the labels are used as x axis labels. If `labels` is `"names"` or `"numbers"`, the variable names are used as labels, the difference being that with `"numbers"`, the variable names are converted to numbers, if possible. Variable names of the forms "number" or "number text" (where the space is optional), are handled.

The argument `pretty.xlabels` is only used when `labels` is specified for a line plot. If `TRUE` (default), the code tries to use a ‘pretty’ selection of labels. If `labels` is `"numbers"`, it also uses the numerical values of the labels for horisontal spacing. If one has excluded parts of the spectral region, one might therefore want to use `pretty.xlabels = FALSE`.

### 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 `...`.

Tip: If the labels specified with `labels` are too long, they get clipped at the border of the plot region. This can be avoided by supplying the graphical parameter `xpd = TRUE` in the plot call.

The handling of `labels` and `pretty.xlabels` in `coefplot` is experimental.

### Author(s)

Ron Wehrens and Bjørn-Helge Mevik

### References

Martens, H., Martens, M. (2000) Modified Jack-knife Estimation of Parameter Uncertainty in Bilinear Modelling by Partial Least Squares Regression (PLSR). Food Quality and Preference, 11(1–2), 5–16.

### See Also

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

### Examples

    data(yarn)
    mod <- plsr(density ~ NIR, ncomp = 10, data = yarn)
    ## 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 2.7-1 Index]