coefplot {pls}

Plot Regression Coefficients of PLSR and PCR models

Description

Function to plot the regression coefficients of an mvr object.

Usage

coefplot(
  object,
  ncomp = object$ncomp,
  comps,
  intercept = FALSE,
  separate = FALSE,
  se.whiskers = FALSE,
  nCols,
  nRows,
  labels,
  type = "l",
  lty,
  lwd = NULL,
  pch,
  cex = NULL,
  col,
  legendpos,
  xlab = "variable",
  ylab = "regression coefficient",
  main,
  pretty.xlabels = TRUE,
  xlim,
  ylim,
  ask = nRows * nCols < nPlots && dev.interactive(),
  ...
)

Arguments

object

an mvr object. The fitted model.

ncomp, comps

vector of positive integers. The components to plot. See coef.mvr for details.

intercept

logical. Whether coefficients for the intercept should be plotted. Ignored if comps is specified. Defaults to FALSE. See coef.mvr for details.

separate

logical. If TRUE, coefficients for different model sizes are blotted in separate plots.

se.whiskers

logical. If TRUE, whiskers at plus/minus 1 estimated standard error are added to the plot. This is only available if the model was cross-validated with jackknife = TRUE. Also, in the current implementation, intercept must be FALSE, and separate must be TRUE if length(ncomp) > 1.

nCols, nRows

integer. The number of coloumns and rows the plots will be laid out in. If not specified, coefplot tries to be intelligent.

labels

optional. Alternative x axis labels. See Details.

type

character. What type of plot to make. Defaults to "l" (lines). Alternative types include "p" (points) and "b" (both). See plot for a complete list of types.

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 separate is TRUE. If present, a legend is drawn at the given position. The position can be specified symbolically (e.g., legendpos = "topright"). This requires >= 2.1.0. Alternatively, the position can be specified explicitly (legendpos = t(c(x,y))) or interactively (legendpos = locator()). This only works well for plots of single-response models.

xlab, ylab

titles for x and y axes. Typically character strings, but can be expressions (e.g., expression(R^2) or lists. See title for details.

main

optional main title for the plot. See Details.

pretty.xlabels

logical. If TRUE, coefplot tries to plot the x labels more nicely. See Details.

xlim, ylim

optional vector of length two, with the x or y limits of the plot.

ask

logical. Whether to ask the user before each page of a plot.

...

Further arguments sent to the underlying plot functions.

Details

coefplot handles multiple responses by making one plot for each response. If separate is TRUE, separate plots are made for each combination of model size and response. The plots are laid out in a rectangular fashion.

If legendpos is given, a legend is drawn at the given position (unless separate is TRUE).

The argument labels can be a vector of labels or one of "names" and "numbers". 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 main can be used to specify the main title of the plot. It is handled in a non-standard way. If there is only on (sub) plot, main will be used as the main title of the plot. If there is more than one (sub) plot, however, the presence of main will produce a corresponding ‘global’ title on the page. Any graphical parametres, e.g., cex.main, supplied to coefplot will only affect the ‘ordinary’ plot titles, not the ‘global’ one. Its appearance can be changed by setting the parameters with par, which will affect both titles. (To have different settings for the two titles, one can override the par settings with arguments to coefplot.)

The argument pretty.xlabels is only used when labels is specified. 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.

When separate is TRUE, the arguments lty, col, and pch default to their par() setting. Otherwise, the default for all of them is 1:nLines, where nLines is the number of model sizes specified, i.e., the length of ncomp or comps.

The function can also be called through the mvr plot method by specifying plottype = "coefficients".

Note

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

The handling of labels and pretty.xlabels is experimental.

Author(s)

Ron Wehrens and Bjørn-Helge Mevik

See Also

mvr, plot.mvr, coef.mvr, plot, legend

Examples

data(yarn)
mod.nir <- plsr(density ~ NIR, ncomp = 8, data = yarn)
## Not run: 
coefplot(mod.nir, ncomp = 1:6)
plot(mod.nir, plottype = "coefficients", ncomp = 1:6) # Equivalent to the previous
## Plot with legend:
coefplot(mod.nir, ncom = 1:6, legendpos = "bottomright")

## End(Not run)

data(oliveoil)
mod.sens <- plsr(sensory ~ chemical, ncomp = 4, data = oliveoil)
## Not run: coefplot(mod.sens, ncomp = 2:4, separate = TRUE)