How to do it...

1. Set the alpha parameter to apply alpha blending to ggplot:

> library(ggplot2)
> sca1 <- ggplot( iris, aes( x = Petal.Length, y = Petal.Width))
> sca1 + geom_point( alpha = .5 , 
                     aes(shape = Species, colour = Species))

The following figure 2.7 shows alpha blending working:

Figure 2.7 - alpha blending with ggplot2.

1. Setting alpha parameter with  plotly will also apply alpha blending:

> library(plotly)
> sca9 <- plot_ly( iris, x = ~Petal.Length, y = ~Petal.Width, 
>                  type = 'scatter', mode = 'markers', alpha = .5, symbol = ~Species)
> sca9

1. ggvis applies alpha blending when opacity argument is set:

> library(ggvis)
> sca3 <- ggvis(iris, x = ~Petal.Length, y = ~Petal.Width)
> sca3 %>% layer_points(opacity := .5, shape = ~Species, fill = ~Species)

Notice that opacity had to be declared using := instead of =.