scoreplot  R Documentation 
Functions to make scatter plots of scores or correlation loadings, and scatter or line plots of loadings.
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, ... )
object 
an object. The fitted model. 
... 
further arguments sent to the underlying plot function(s). 
comps 
integer vector. The components to plot. 
labels 
optional. Alternative plot labels or x axis labels. See Details. 
identify 
logical. Whether to use 
type 
character. What type of plot to make. Defaults to 
xlab, ylab 
titles for x and y axes. Typically character
strings, but can be expressions or lists. See 
x 
a 
scatter 
logical. Whether the loadings should be plotted as a scatter instead of as lines. 
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 
pretty.xlabels 
logical. If 
xlim 
optional vector of length two, with the x limits of the plot. 
plotx 
locical. Whether to plot the X correlation loadings.
Defaults to 
ploty 
locical. Whether to plot the Y correlation loadings.
Defaults to 
radii 
numeric vector, giving the radii of the circles drawn in

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
.
The functions return whatever the underlying plot function (or
identify
) returns.
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.
Ron Wehrens and BjørnHelge Mevik
Martens, H., Martens, M. (2000) Modified Jackknife Estimation of Parameter Uncertainty in Bilinear Modelling by Partial Least Squares Regression (PLSR). Food Quality and Preference, 11(1–2), 5–16.
mvr
, plot.mvr
, scores
,
loadings
, identify
, legend
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)
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