Question

I am trying to plot several features of a group of samples to various aesthetics. Border color and size of a circle is one of them. However, if I try to set a larger baseline border for these shapes, by setting lwd=2, the shapes all revert to the same size and the legend is gone. I just want the circles to have a larger border, how can I do this?

An example:

library(ggplot2)
testFrame <- data.frame(
  sizeVar=factor(c('a', 'a', 'a', 'a', 'b', 'b', 'b', 'b')),
  samples=rep(c('Sample1', 'Sample2'), times=4),
  features=c(rep('Feature1', times=4), rep('Feature2', times=4))
)
testPlot <- ggplot(data=testFrame, aes(x=samples, y=features))
testPlot + 
    geom_point(aes(size=sizeVar), pch=21, color='black', fill='gray') +
    scale_size_manual(values=c(9,4)) + theme_bw()
testPlot + 
   geom_point(aes(size=sizeVar), pch=21, lwd=3, color='black', fill='gray') + 
   scale_size_manual(values=c(9,4)) + theme_bw()

Answer 1

Start with your graph:

> testPlot + 
    geom_point(aes(size=sizeVar), pch=21, color='black', fill='gray') +
    scale_size_manual(values=c(9,4)) + theme_bw()

List the elements:

> grid.ls()

GRID.gTableParent.162
  background.1-6-6-1
  spacer.4-3-4-3
  panel.3-4-3-4
    grill.gTree.126
      panel.background.rect.121
      panel.grid.major.y.polyline.123
      panel.grid.major.x.polyline.125
    geom_point.points.116
    panel.border.rect.118
  axis-l.3-3-3-3
    axis.line.y.zeroGrob.136
    axis
  axis-b.4-4-4-4
    axis.line.x.zeroGrob.130
    axis
  xlab.5-4-5-4
  ylab.3-2-3-2
  guide-box.3-5-3-5
  title.2-4-2-4

Now to change the appropriate element:

> grid.edit("geom_point.points", grep=TRUE, gp=gpar(lwd=3))