Plot Regression Coefficients of PLSR and PCR models
Function to plot the regression coefficients of an mvr object.
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(), ...)object |
an |
ncomp, comps |
vector of positive integers. The components to
plot. See |
separate |
logical. If |
se.whiskers |
logical. If |
intercept |
logical. Whether coefficients for the intercept should
be plotted. Ignored if |
nCols, nRows |
integer. The number of coloumns and rows the
plots will be laid out in. If not specified, |
labels |
optional. Alternative x axis labels. See Details. |
type |
character. What type of plot to make. Defaults to
|
lty |
vector of line types (recycled as neccessary). Line types can be
specified as integers or character strings (see |
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
|
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 |
legendpos |
Legend position. Optional. Ignored if |
xlab,ylab |
titles for x and y axes. Typically
character strings, but can be expressions (e.g.,
|
main |
optional main title for the plot. See Details. |
pretty.xlabels |
logical. If |
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. |
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".
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.
Ron Wehrens and Bjørn-Helge Mevik
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)
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