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<table width="100%" summary="page for scoreplot {pls}"><tr><td>scoreplot {pls}</td><td align="right">R Documentation</td></tr></table>
<h2>Plots of Scores, Loadings and Correlation Loadings</h2>
<h3>Description</h3>
<p>
Functions to make scatter plots of scores or correlation loadings, and
scatter or line plots of loadings.
</p>
<h3>Usage</h3>
<pre>
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, radii = c(sqrt(1/2), 1),
identify = FALSE, type = "p", xlab, ylab, ...)
</pre>
<h3>Arguments</h3>
<table summary="R argblock">
<tr valign="top"><td><code>object</code></td>
<td>
an <font face="Courier New,Courier" color="#666666"><b>R</b></font> object. The fitted model.</td></tr>
<tr valign="top"><td><code>comps</code></td>
<td>
integer vector. The components to plot.</td></tr>
<tr valign="top"><td><code>scatter</code></td>
<td>
logical. Whether the loadings should be plotted as a
scatter instead of as lines.</td></tr>
<tr valign="top"><td><code>labels</code></td>
<td>
optional. Alternative plot labels or <i>x</i> axis labels.
See Details.</td></tr>
<tr valign="top"><td><code>radii</code></td>
<td>
numeric vector, giving the radii of the circles drawn in
<code>corrplot</code>. The default radii represent 50% and 100%
explained variance of the <i>X</i> variables by the chosen components.</td></tr>
<tr valign="top"><td><code>identify</code></td>
<td>
logical. Whether to use <code>identify</code> to
interactively identify points. See below.</td></tr>
<tr valign="top"><td><code>type</code></td>
<td>
character. What type of plot to make. Defaults to
<code>"p"</code> (points) for scatter plots and <code>"l"</code> (lines) for
line plots. See <code><a href="../../Zelig/html/plot.zelig.html">plot</a></code> for a complete list
of types (not all types are possible/meaningful for all plots).</td></tr>
<tr valign="top"><td><code>lty</code></td>
<td>
vector of line types (recycled as neccessary). Line types can be
specified as integers or character strings (see <code><a href="../../graphics/html/par.html">par</a></code>
for the details).</td></tr>
<tr valign="top"><td><code>lwd</code></td>
<td>
vector of positive numbers (recycled as neccessary), giving
the width of the lines.</td></tr>
<tr valign="top"><td><code>pch</code></td>
<td>
plot character. A character string or a vector of
single characters or integers (recycled as neccessary). See
<code><a href="../../graphics/html/points.html">points</a></code> for all alternatives.</td></tr>
<tr valign="top"><td><code>cex</code></td>
<td>
numeric vector of character expansion sizes (recycled as
neccessary) for the plotted symbols.</td></tr>
<tr valign="top"><td><code>col</code></td>
<td>
character or integer vector of colors for plotted lines and
symbols (recycled as neccessary). See <code><a href="../../graphics/html/par.html">par</a></code> for the details.</td></tr>
<tr valign="top"><td><code>legendpos</code></td>
<td>
Legend position. Optional. Ignored if <code>scatter</code> is
<code>TRUE</code>. If present, a legend is drawn at the given position.
The position can be specified symbolically (e.g., <code>legendpos =
"topright"</code>). This requires <font face="Courier New,Courier" color="#666666"><b>R</b></font> >= 2.1.0. Alternatively, the
position can be specified explicitly (<code>legendpos = t(c(x,y))</code>)
or interactively (<code>legendpos = <a href="../../graphics/html/locator.html">locator</a>()</code>).</td></tr>
<tr valign="top"><td><code>xlab,ylab</code></td>
<td>
titles for <i>x</i> and <i>y</i> axes. Typically
character strings, but can be expressions or lists. See
<code><a href="../../graphics/html/title.html">title</a></code> for details.</td></tr>
<tr valign="top"><td><code>pretty.xlabels</code></td>
<td>
logical. If <code>TRUE</code>, <code>loadingplot</code>
tries to plot the <i>x</i> labels more nicely. See Details.</td></tr>
<tr valign="top"><td><code>xlim</code></td>
<td>
optional vector of length two, with the <i>x</i> limits of
the plot.</td></tr>
<tr valign="top"><td><code>x</code></td>
<td>
a <code>scores</code> or <code>loadings</code> object. The scores or
loadings to plot.</td></tr>
<tr valign="top"><td><code>...</code></td>
<td>
further arguments sent to the underlying plot function(s).</td></tr>
</table>
<h3>Details</h3>
<p>
<code>plot.scores</code> is simply a wrapper calling <code>scoreplot</code>,
passing all arguments. Similarly for <code>plot.loadings</code>.
</p>
<p>
<code>scoreplot</code> is generic, currently with a default method that
works for matrices and any object for which <code><a href="scores.html">scores</a></code>
returns a matrix. The default <code>scoreplot</code> 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 <code>identify</code> is <code>TRUE</code>, the
function <code><a href="../../graphics/html/identify.html">identify</a></code> is used to interactively identify
points.
</p>
<p>
Also <code>loadingplot</code> is generic, with a default method that works
for matrices and any object where <code><a href="scores.html">loadings</a></code> returns a
matrix. If <code>scatter</code> is <code>TRUE</code>, the default method works exactly
like the default <code>scoreplot</code> method. Otherwise, it makes a lineplot of the selected
loading vectors, and if <code>identify</code> is <code>TRUE</code>,
uses <code><a href="../../graphics/html/identify.html">identify</a></code> to interactively identify points. Also,
if <code>legendpos</code> is given, a legend is drawn at the position
indicated.
</p>
<p>
<code>corrplot</code> works exactly like the default <code>scoreplot</code>
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 <code>radii</code>. Each
point corresponds to an <i>X</i> 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
<code>radii</code> corresponds to 50% and 100% explained variance.
</p>
<p>
<code>scoreplot</code>, <code>loadingplot</code> and <code>corrplot</code> can also be
called through the plot method for <code>mvr</code> objects, by specifying
<code>plottype</code> as <code>"scores"</code>, <code>"loadings"</code> or
<code>"correlation"</code>, respectively. See <code><a href="plot.mvr.html">plot.mvr</a></code>.
</p>
<p>
The argument <code>labels</code> can be a vector of labels or one of
<code>"names"</code> and <code>"numbers"</code>.
</p>
<p>
If a scatter plot is produced (i.e., <code>scoreplot</code>, <code>corrplot</code>, or
<code>loadingplot</code> with <code>scatter = TRUE</code>), the labels
are used instead of plot symbols for the points plotted. If
<code>labels</code> is <code>"names"</code> or <code>"numbers"</code>, the row
names or row numbers of the matrix (scores, loadings or correlation
loadings) are used.
</p>
<p>
If a line plot is produced (i.e., <code>loadingplot</code>), the labels are
used as <i>x</i> axis labels. If <code>labels</code> is <code>"names"</code> or
<code>"numbers"</code>, the variable names are used as labels, the
difference being that with <code>"numbers"</code>, the variable names are
converted to numbers, if possible. Variable names of the forms
<SAMP>"number"</SAMP> or <SAMP>"number text"</SAMP> (where the space is optional),
are handled.
</p>
<p>
The argument <code>pretty.xlabels</code> is only used when <code>labels</code> is
specified for a line plot. If <code>TRUE</code> (default), the code tries
to use a ‘pretty’ selection of labels. If <code>labels</code> is
<code>"numbers"</code>, 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 <code>pretty.xlabels = FALSE</code>.
</p>
<h3>Value</h3>
<p>
The functions return whatever the underlying plot function (or
<code>identify</code>) returns.</p>
<h3>Note</h3>
<p>
<code><a href="../../PerformanceAnalytics/html/PerformanceAnalytics-internal.html">legend</a></code> has many options. If you want greater
control over the appearance of the legend, omit the <code>legendpos</code>
argument and call <code>legend</code> manually.
</p>
<p>
Graphical parametres (such as <code>pch</code> and <code>cex</code>) can also
be used with <code>scoreplot</code> and <code>corrplot</code>. They are not
listed in the argument list simply because they are not handled
specifically in the function (unlike in <code>loadingplot</code>), but
passed directly to the underlying plot functions by <code>...</code>.
</p>
<p>
The handling of <code>labels</code> and <code>pretty.xlabels</code> in
<code>coefplot</code> is experimental.
</p>
<h3>Author(s)</h3>
<p>
Ron Wehrens and Bj鴕n-Helge Mevik
</p>
<h3>References</h3>
<p>
Martens, H., Martens, M. (2000) Modified Jack-knife Estimation of
Parameter Uncertainty in Bilinear Modelling by Partial Least Squares
Regression (PLSR).
<EM>Food Quality and Preference</EM>, <B>11</B>(1–2), 5–16.
</p>
<h3>See Also</h3>
<p>
<code><a href="mvr.html">mvr</a></code>, <code><a href="plot.mvr.html">plot.mvr</a></code>,
<code><a href="scores.html">scores</a></code>, <code><a href="scores.html">loadings</a></code>, <code><a href="../../graphics/html/identify.html">identify</a></code>,
<code><a href="../../PerformanceAnalytics/html/PerformanceAnalytics-internal.html">legend</a></code>
</p>
<h3>Examples</h3>
<pre>
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)
</pre>
<hr><div align="center">[Package <em>pls</em> version 2.0-1 <a href="00Index.html">Index]</a></div>
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