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copied!<h2>The problem</h2> <p>This does appear to be a bug, but it's a problem with <code>pdf()</code> and not with <code>Sweave()</code> itself. </p> <p>To see what I mean, try this call to <code>pdf()</code>. It produces the same defective plot displayed above:</p> <pre><code>pdf("pdfPlot.pdf") plot(0.5, 0.5, xlim = c(0,1), ylim = c(0,1)) legend("bottomright", c("data", "summary", "curve", "conf. region"), pch = c(2,1,NA,NA), lwd = c(NA,NA, 2,1)) dev.off() </code></pre> <p>By contrast, <code>cairo_pdf()</code> produces a plot that looks just fine:</p> <pre><code>cairo_pdf("cairo_pdfPlot.pdf") plot(0.5, 0.5, xlim = c(0,1), ylim = c(0,1)) legend("bottomright", c("data", "summary", "curve", "conf. region"), pch = c(2,1,NA,NA), lwd = c(NA,NA, 2,1)) dev.off() </code></pre> <h2>Solution 1: Use knitr.</h2> <p>If you are willing to make the switch to <code>knitr</code>, fixing this is easy. Just add <code>dev="cairo_pdf"</code> to your code chunk header (and, if you like, drop the <code>fig=TRUE</code>), like this:</p> <pre><code><<dev="cairo_pdf">>= ... ... @ </code></pre> <p>Processing the code is then as simple as doing <code>library(knitr); knit("myScript.Rnw")</code> in place of your current call to <code>Sweave("myScript.Rnw")</code></p> <h2>Solution 2: Construct your own call to \includegraphics{}.</h2> <p>If you must stick with <code>Sweave()</code>, doing something like this will get you around the problem:</p> <pre><code><<results=tex, term=FALSE, echo=FALSE>>= cairo_pdf("myPlot.pdf", width=5) plot(0.5, 0.5, xlim = c(0,1), ylim = c(0,1)) legend("bottomright", c("data", "summary", "curve", "conf. region"), pch = c(2,1,NA,NA), lwd = c(NA,NA, 2,1)) dev.off() cat("\\includegraphics{myPlot.pdf}\n\n") @ </code></pre>

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