Part of the problem is that alpha is a new and undocumented feature
(note to developers: add this info into the pdf and rgb documentation).
It only works in PDFs (maybe on quartz on Macs?), so you need to write
to a PDF file:
pdf("out.pdf",version="1.4")
plot(1:10,col=rgb(1,0,0,alpha=seq(0,1,length.out=10)))
dev.off()
Now open up the PDF file...
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and provide commented, minimal, self-contained, reproducible code.
