R ggplot barplot; Fill based on two separate variables

Question

A picture says more than a thousand words. As you can see, my fill is based on the variable variable.

Within each bar there is however mul

Answer 1

You might need to separate your Method and variable factors. Here are two ways to do that:

Use facet_wrap():

    ggplot(short.m, aes(x=variable, y=value/100, fill=Complexity)) + 
    facet_wrap(~ Method) + geom_bar(position="stack", colour="black") +
    scale_alpha_manual(values=c(0.1, 0.5, 1)) + coord_flip()

Use both on the x-axis:

    ggplot(short.m, aes(x=Method:variable, y=value/100, group=Method, fill=variable, alpha=Complexity,)) + 
    geom_bar(stat="identity", position="stack", colour="black") +
    scale_alpha_manual(values=c(0.1, 0.5, 1)) + coord_flip()