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are you using Waterfall() or waterfall(), theres currently two function while I transition to a more object oriented style.
If you're using Waterfall() this should work:
plot <- Waterfall() pdf(file="tmp.pdf") drawPlot(plot) dev.off()
otherwise you should be able to do this:
pdf(file="tmp.pdf") waterfall() dev.off()
Both functions have the ability to add extra ggplot layers for lower case waterfall something like this should work:
library(ggplot2) layer <- list(ggtitle("MY TITLE")) waterfall(brcaMAF, mainRecurCutoff = .5, mutBurdenLayer = layer)
There is a similar parameter for the new uppercase Waterfall() function as well, you just need to make sure your ggplot layer is passed as a list.