plotShifts: plotShifts

In hferg/BTprocessR: A set of tools to help with the interpretation and analysis of the output of BayesTraits MCMC analyses.

Description

Plots the locations of the origins of scalars from the postprocessor output of bayestraits.

Usage

plotShifts(PP, plot.options = list(), ...)

Arguments

PP	The output of the rjpp function.
plot.options	A list of control options. See details.
...	Additional arguments passed to plotPhylo

Details

The default behaviour of plotShifts depends on the transformations present in the rjpp output. If variable rates, then 3 trees will be plotted: the first has branches coloured according the log of the mean rate, the second shows all node scalars present more than once in the posterior, coloured according to the mean log rate and the third shows the same for branch scalars. If delta, kappa or lambda are present then a single tree is plotted showing all nodes that receive a scalar, coloured according to mean magnitude. If multiple transformations are present then the user will be prompted to select one. The plot.options list provides a high degree of control over what is plotted, allowing the default behaviour to be customised. The options, and values that they can take, are as follows.

• threshold: [0-1] The threshold of presence in the posterior over which a node and/or branch scalar is plotted. Also the threshold referenced by coloured.edges and scaled.edges.

• transformation: [rate, delta, lambda, kappa] The transformation to plot.

• edge.colour: [none, mean, median, mode, sd, scale_pc] The metric to colour edges by. If none branches default to the na.colour option. Mean, median, mode and sd correspond to the appropriate branch lengths from the posterior of trees and scale_pc colours edges according to the percentage of time they are scaled in the posterior.

• edge.transparency: [none, scale_pc, sd] The measure to make edges proportionally transparent by. None results in uniform solid branches, scale_pc gives edges that are scaled less frequently in the posterior higher transparency, and sd gives branches that have higher SD of estimated branch lengths more solid colours.

• coloured.edges: [all, threshold] The edges to colour. If "all" then all edges are coloured according to edge.colour, otherwise if "threshold" then only edges that are scaled over the specified threshold are coloured. Uncoloured edges default to na.colour

• edge.palette: [viridis, magma, inferno, plasma, viridis, c("<colour1>", "<colour2>")] The colour palette for edges. If not using a named palette then a vector of at least two colours must be specified - the first will be the low end of the palette and the last the top end. Any other colours in the vector will be included in the gradient.

• edge.scale: [none, mean, median, mode]

• scaled.edges: [all, threshold]

• node.colour: []

• node.scale: []

• node.transparency: []

• node.palette: [viridis, magma, inferno, plasma, viridis, c("<colour1>", "<colour2>")] The colour palette for node symbols. If not using a named palette then a vector of at least two colours must be specified - the first will be the low end of the palette and the last the top end. Any other colours in the vector will be included in the gradient.

• node.fill: []

• node.border: []

• node.shape: ["circle"] The shape for the node labels - "circle", "square", "diamond", "uptriangle", "downtriangle".

• node.cex: [0-??] The scaling factor for node symbols. This is the scaling factor that the symbols start at before any subsequent scaling (i.e. if a node symbol receives no scaling, this is what it's scaling factor will be.)

• branch.colour: []

• branch.transparency: []

• branch.palette: [viridis, magma, inferno, plasma, viridis, c("<colour1>", "<colour2>")] The colour palette for branch symbols. If not using a named palette then a vector of at least two colours must be specified - the first will be the low end of the palette and the last the top end. Any other colours in the vector will be included in the gradient.

• branch.fill: []

• branch.border: []

• branch.scale: []

• branch.shape: ["circle"] The shape for the branch labels - "circle", "square", "diamond", "uptriangle", "downtriangle".

• branch.cex: [0-??] The scaling factor for branch symbols. This is the scaling factor that the symbols start at before any subsequent scaling (i.e. if a branch symbol receives no scaling, this is what it's scaling factor will be.

• na.colour: []

• layout: [c("e", "n", "b")] This controls the layout of the plots. The option takes the form of a vector of letters - "e", "n" and/or "b". Each element of the vector is a new panel in the plot, and the composition of letters in the element determins whether coloured edges - "e" - node labels - "n" - and/or branch labels - "b" - are plotted. e.g. c("e", "n", "b") gives a three panel plot - one panel with coloured edges, one with node labels and one with branch labels. c("en", "b") produces two plots - one with coloured edges and node labels and one with branch labels. c("enb") produces a single plot with edges, node labels and branch labels.

• show.legend: [TRUE, FALSE] Whether or not to show legends. Legends can be drawn seperately using the plotLegends function and then added to plots using some other graphics software. This is useful if the legend butts up against the lower branches of scaled phylogenies, if the type = "fan" option is used (the automatic legend placement puts it in a weird place) or if a more complex legend is needed (e.g. a histogram).

• legend.pos: [auto, c(xl, yb, xr, yt)] The legend position on the plot. If "auto" then the legend position will be in the bottom right at "best guess" coordinates. Otherwise a vector of coordinates for bottom left and top right corner of the legend.

• legend: []

• save.plot: [TRUE, FALSE] If TRUE then the plot will be saved to the working directory as a pdf and NOT plotted to the screen.

• filename: [<some_filename>] The filename to save the plot to. If not specified then a filename will be generated based on the time and date. There's no need to specify file extension.

• plot.size: [c(<width>, <height>)] The width and height of the saved plot. If plot.format = "png" then the unit is in pixels.

• legend.only [TRUE, FALSE] When TRUE only the legend(s) corresponding to all the other options are plotted. When this option is called two legends are plotted per plot - the one that normally appears on the plot, and one accompanied by a histogram showing the same data used to generate the colours. This option is useful for when the legend is to be combined with the plot in seperate graphical software (e.g. GIMP, Inkscape). This option is compatible with save.plot.

hferg/BTprocessR documentation built on March 8, 2020, 11:45 a.m.