i have a problem and want to ask a question .how to save picture and add a title to waterfall mutation analyse by GenVisR  package?

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.