Plotting functions to visualize the results of a SURFACE analysis, with colors depicting regime structure: surfaceTreePlot produces a customized plot.phylo figure, and surfaceTraitPlot produces a scatterplot of trait values and optima
surfaceTreePlot(tree, hansenfit, cols = NULL, convcol = TRUE, labelshifts = FALSE, ...)
surfaceTraitPlot(dat, hansenfit, whattraits = c(1, 2), cols = NULL,
convcol = TRUE, pchs = c(21, 21), cex.opt = 2.5, optellipses = FALSE,
ellipsescale = 1, flatten1D = FALSE, add = FALSE, ypos = 0,
plotoptima = TRUE, plottraits = TRUE, y.lim = NULL, x.lim = NULL,
y.lab = NULL, x.lab = NULL, ...)Creates one tree or trait plot on the current graphics device
Phylogenetic tree in phylo format
Trait data formatted as a data frame with named rows and at least two columns
An object containing the fitted Hansen model to use in plotting, with elements fit and savedshifts. This may be the list produced by any one iteration of surfaceForward or surfaceBackward, or the list produced by surfaceSimulate
A two-element integer (or a single integer; see Details) indicating which traits to use for the (x,y) axes of a trait plot (defaults to c(1,2))
An optional character vector of colors for painting branches in surfaceTreePlot or coloring symbols in surfaceTraitPlot. One color should be provided per regime in hansenfit; if cols=NULL the function will attempt an appropriate default
A logical indicating whether to select separate colors for convergent (colorful) and non-convergent (greyscale) regimes (defaults to TRUE)
A logical indicating whether to add integer labels to branches in the tree to show the order in which regime shifts were added in the forward phase (defaults to FALSE)
Vector with two integers representing the plotting characters to use for trait values and optima, respectively, in surfaceTraitPlot; both default to 21 (filled circles)
Character expansion for symbols representing the optima in surfaceTraitPlot; defaults to 2.5 (symbols representing data points can be specified with cex)
A logical indicating whether to draw ellipses based on the fitted OU model instead of denoting optimum positions with pchs and cex.opt. The ellipses are drawn as the optima +/- the standard deviation of the stationary distribution of the inferred OU process: sigma_squared/(2*alpha), multiplied by ellipsescale
A scalar or vector indicating how many standard deviations to draw ellipses above and below the optima; if a vector, concentric ellipses of various sizes will be drawn; defaults to 1
A logical indicating whether all regimes should be placed on a single line when surfaceTraitPlot is called for a single trait; defaults to FALSE
A logical indicating whether to add a new element to an existing surfaceTraitPlot graph instead of creating a new one; defaults to FALSE
Position on the y axis to place the traits and optima on; only applies if a single trait is used and flatten1D = TRUE
A logical indicating whether the optima should be displayed in surfaceTraitPlot; defaults to TRUE
A logical indicating whether the trait values should be displayed in surfaceTraitPlot; defaults to TRUE
Lower and upper limits for the y-axis; by default will be calculated to fit all points and ellipses fit in the frame
Lower and upper limits for the x-axis; by default will be calculated to fit all points and ellipses fit in the frame
y-axis label; defaults to the column name in the data frame
x-axis label; defaults to the column name in the data frame
Additional arguments to be passed to the plot or points functions
Travis Ingram
For trait plots using the option optellipses=TRUE, note that in some cases (e.g. if alpha is very small) the ellipses will not convey useful information. If trait data are unidimensional, or if whattraits is provided as a single integer, data will be plotted on the x-axis and the y-axis will separate different regimes (and ellipse width in the y-dimension will not be meaningful)
Ingram, T. & Mahler, D.L. (2013) SURFACE: detecting convergent evolution from comparative data by fitting Ornstein-Uhlenbeck models with stepwise AIC. Methods in Ecology and Evolution 4: 416-425.
Mahler, D.L., Ingram, T., Revell, L.J. & Losos, J.B. (2013) Exceptional convergence on the macroevolutionary landscape in island lizard radiations. Science 341: 292-295.
surfaceForward, surfaceBackward, surfaceSimulate, surfaceSummary, surfaceAICPlot
data(surfaceDemo)
tree<-surfaceDemo$tree
dat<-surfaceDemo$sim$dat
olist<-convertTreeData(tree,dat)
otree<-olist[[1]]; odata<-olist[[2]]
startmod<-startingModel(otree, odata, shifts = c("6"="b"))
surfaceTreePlot(tree,startmod[[1]],labelshifts=TRUE,cols=c("black","red"))
surfaceTraitPlot(dat,startmod[[1]],whattraits=c(1,2),cols=c("black","red"))
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