setMap: Set color map for various phylogenetic objects of classes

In phytools: Phylogenetic Tools for Comparative Biology (and Other Things)

Set color map for various phylogenetic objects of classes

Description

Changes the color map (ramp) in an object of class "contMap", "densityMap", "phyloScattergram", or "multirateBM_plot".

Usage

setMap(x, ...)
## S3 method for class 'contMap'
setMap(x, ...)
## S3 method for class 'densityMap'
setMap(x, ...)
## S3 method for class 'phyloScattergram'
setMap(x, ...)
## S3 method for class 'multirateBM_plot'
setMap(x, ...)

Arguments

x	an object of various special types containing a phylogenetic tree. See Description for more details.
...	arguments to be passed to colorRampPalette. Also, the argument invert which (if invert=TRUE) will just flip the current color ramp.

Value

An object of class "contMap", "densityMap", "phyloScattergram", or "multirateBM_plot".

Author(s)

Liam Revell [e-mail]

References

Revell, L. J. (2012) phytools: An R package for phylogenetic comparative biology (and other things). Methods Ecol. Evol., 3, 217-223.

Revell, L. J. (2013) Two new graphical methods for mapping trait evolution on phylogenies. Methods in Ecology and Evolution, 4, 754-759.

Revell, L. J. (2014) Graphical methods for visualizing comparative data on phylogenies. Chapter 4 in Modern phylogenetic comparative methods and their application in evolutionary biology: Concepts and practice (L. Z. Garamszegi ed.), pp. 77-103.

Revell, L. J. (2024) phytools 2.0: an updated R ecosystem for phylogenetic comparative methods (and other things). PeerJ, 12, e16505.

See Also

contMap, densityMap, multirateBM

phytools documentation built on Nov. 5, 2025, 5:11 p.m.