title: SpatialPolygonsDataFrame doesn't plot properly when I make the color transparent
body: <p>I've been struggling with this problem for a few days. I have a shapefile that contains zip code polygons. I'm trying to plot a certain portion of it with a transparent color (<code>alpha=0.7</code>), but some of the polygons at the edge of the plot end up with no color. If <code>alpha=1.0</code>, all polygons are fine. The shapefile is stored as a Large <code>SpatialPolygonsDataFrame</code>. </p>
  
  <pre><code># Code that you can use (Thanks jbaums)
  
  library(rgdal);
  download.file('http://www.naturalearthdata.com/http//www.naturalearthdata.com/do‌​wnload/110m/cultural/ne_110m_admin_0_countries.zip', {f &lt;- tempfile()}); 
  unzip(f, exdir=tempdir()); 
  shp &lt;- readOGR(tempdir(), 'ne_110m_admin_0_countries'); 
  plot(shp, col='#FF000070', xlim=c(-100, 25))
  </code></pre>
  
  <p>For reference, my code looks like this :</p>
  
  <pre><code>#~~~ Read zip shapefile
    in_zip.shp  = "./Data/USZIP11_wSTCntyLLFIPS.shp"
    zip_poly = readShapePoly(in_zip.shp)
  
  #~~~ Set-up the mapping parameters
    xlim = c(-82.0, -80.7)
    ylim = c(25.5, 26.8)
  
  #~~~ Works well
    output_figure &lt;- "./Good.png"
    png(output_figure, width=5, height=4, units="in", res=1200)
    par(mar=c(1.5, 1.8, 2.0, 0.7))
    plot(xlim, ylim, type="n", xlim=xlim, ylim=ylim, axes=FALSE, xlab="", ylab="")
  
    plot(zip_poly, col=rgb(1, 0, 0, alpha=1), xlim=xlim, ylim=ylim, lty=1.3, add=T)
    box()
    title(main="Good")
    dev.off()
  
  #~~~ Doesn't work well
    output_figure &lt;- "./Bad.png"
    png(output_figure, width=5, height=4, units="in", res=1200)
    par(mar=c(1.5, 1.8, 2.0, 0.7))
    plot(xlim, ylim, type="n", xlim=xlim, ylim=ylim, axes=FALSE, xlab="", ylab="")
  
    plot(zip_poly,col=rgb(1,0,0,alpha=0.7),xlim=xlim,ylim=ylim,lty=1.3,add=T)
    box()
    title(main="Bad")
    dev.off()
  </code></pre>
  
  <p>Any tips would be appreciated. I attached figures so you can see what problem I get with my code. Thanks!</p>
  
  <p><img src="https://i.imgur.com/zT55btr.png" alt="good.png">
  <img src="https://i.imgur.com/dxTcOtx.png" alt="bad.png"></p>