How to overlay RateThroughTime plots

[Daniel David Díaz Contreras Díaz]

Hello everyone,

This may be relatively simple for most experienced users in R plotting, but I am trying to generate something like the image below. I want to overlay different RateThroughTime lines in the same plot. Any hint is greatly appreciated.

Thanks in advance. Best wishes.

Daniel

[Daniel David Díaz Contreras Díaz]

More precisely, as in the letter B, C or D. Thank you

[pasca...@gmail.com]

Hi Daniel,

The examples in the help for plotRateThroughTime() show how to do this.

I would recommend that you first calculate the time-binned rates and then do the plotting. This makes it easier to experiment with the plotting without needing to recalculate the rates each time.

So for example:

library(BAMMtools)

data(events.whales)
data(whales)
ephy <- getEventData(whales,events.whales)

rmat1 <- getRateThroughTimeMatrix(ephy, node = 141, nodetype = 'exclude')
rmat2 <- getRateThroughTimeMatrix(ephy, node = 141, nodetype = 'include')

plotRateThroughTime(rmat1, intervals=seq(from = 0, 0.9, by = 0.01),
    smooth = TRUE, ylim = c(0, 1.2))

plotRateThroughTime(rmat2, intervals = seq(from = 0, 0.9, by = 0.01),
    smooth = TRUE, add = TRUE, intervalCol = 'orange')

To get the proper plot dimensions, you may need to adjust xlim and ylim in the first plot.

And of course you can do this with any number of groups/clades.

If you have more specific questions, let me know.

-Pascal