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Last data update: 2014.03.03

R: Plot distinct rate shift configurations on a phylogeny

plot.bammshifts

R Documentation

Plot distinct rate shift configurations on a phylogeny

Description

Plots a random distinct rate shift configuration sampled by BAMM on a phylogeny.

Usage

## S3 method for class 'bammshifts'
plot(x, ephy, method = "phylogram", pal = "RdYlBu",
  rank = NULL, index = NULL, spex = "s", legend = TRUE,
  add.freq.text = TRUE, logcolor = FALSE, breaksmethod = "linear",
  color.interval = NULL, JenksSubset = 20000, ...)

Arguments

`x`	An object of class `bammshifts`.
`ephy`	An object of class `bammdata`.
`method`	A character string for which plotting method to use. "phylogram" uses rectangular coordinates. "polar" uses polar coordinates.
`pal`	The color palette to use in `plot.bammdata`.
`rank`	The rank of the core shift configuration to plot. For the default (`NULL`) a random configuration is chosen.
`index`	The posterior sample to plot. For the default (`NULL`) a random sample is chosen.
`spex`	A character string indicating what type of macroevolutionary rates should be plotted. "s" (default) indicates speciation rates, "e" indicates extinction rates, and 'netdiv' indicates net diversification rates. Ignored if `ephy$type = "trait"`.
`legend`	Logical indicating whether to plot a legend.
`add.freq.text`	A logical indicating whether the frequency of each sampled shift configuration should be added to each plot.
`logcolor`	Logical. Should colors be plotted on a log scale.
`breaksmethod`	Method used for determining color breaks. See help file for `assignColorBreaks`.
`color.interval`	Min and max value for the mapping of rates. One of the two values can be `NA`. See details in `plot.bammdata` for further details.
`JenksSubset`	If `breaksmethod = "jenks"`, the number of regularly-spaced samples to subset from the full rates vector. Only relevant for large datasets. See help file for `assignColorBreaks`.
`...`	Other arguments to `plot.bammdata`.

Details

A rate shift configuration is the set of nodes of the phylogeny where a shift occurs in the macroevolutionary rate dynamic of diversification or trait evolution. Each posterior sample is a potentially distinct rate shift configuration. Different configurations may imply different macroevolutionary scenarios. This function helps visualize the different distinct rate shift configurations sampled by BAMM.

A core shift configuration is defined by a set of nodes that have shift probabilities that are substantially elevated relative to what you expect under the prior alone. These core configurations are inferred in distinctShiftConfigurations. It is almost certain that more than one core shift configuration will be sampled by BAMM. Moreover, each core shift configuration may contain many subconfigurations. A subconfiguration contains the core shift node configuration and zero or more additional shift nodes that occur with low marginal probability.

Points are added to the branches subtending the nodes of each rate configuration. The size of the point is proportional to the marginal probability that a shift occurs on a specific branch. If the instantaneous rate at a shift's origin represents an initial increase above the ancestral instantaneous rate the point is red. If the instantaneous rate at a shift's origin represents an initial decrease below the ancestral instantaneous rate the point is blue.

Author(s)

Mike Grundler, Dan Rabosky

References

http://bamm-project.org

Examples

data(whales, events.whales)

ed <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)

sc <- distinctShiftConfigurations(ed, expectedNumberOfShifts = 1,
                                  threshold = 5)

plot(sc, ed)

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

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'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(BAMMtools)
Loading required package: ape
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/BAMMtools/plot.bammshifts.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.bammshifts
> ### Title: Plot distinct rate shift configurations on a phylogeny
> ### Aliases: plot.bammshifts
> 
> ### ** Examples
> 
> data(whales, events.whales)
> 
> ed <- getEventData(whales, events.whales, burnin=0.25, nsamples=500)
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  2495000
Analyzing  500  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> sc <- distinctShiftConfigurations(ed, expectedNumberOfShifts = 1,
+                                   threshold = 5)
> 
> plot(sc, ed)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>