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Last data update: 2014.03.03

R: Add a color legend to a phylo-rate plot

addBAMMlegend

R Documentation

Add a color legend to a phylo-rate plot

Description

Add a legend to a phylorate plot, with greater manual control.

Usage

addBAMMlegend(x, direction, side, location = "topleft", nTicks = 2,
  shortFrac = 0.02, longFrac = 0.3, axisOffset = 0.002, cex.axis = 0.8,
  labelDist = 0.7, ...)

Arguments

`x`	A `plot.bammdata` object.
`direction`	Direction of color ramp. If omitted, then direction is automatically inferred, otherwise can be specified as horizontal or vertical.
`side`	Side for tick marks, see `axis` documentation. Automatically inferred if omitted.
`location`	Either a location name (see Details), or coordinates for the corners of the bar legend c(xmin, xmax, ymin, ymax).
`nTicks`	Number of tick marks, besides min and max.
`shortFrac`	Percent of the plot width range that will be used as the short dimention of the legend. Only applies to preset location options.
`longFrac`	Percent of the plot width range that will be used as the long dimension of the legend. Only applies to preset location options.
`axisOffset`	Distance from color bar for labels, as a percent of the plot width.
`cex.axis`	Size of axis labels.
`labelDist`	Distance from axis to axis labels (passed to mgp).
`...`	Additional parameters to be passed to axis.

Details

A number of predefined locations exist in this function to make it easy to add a legend to a phylorate plot. Preset locations are: topleft, topright, bottomleft, bottomright, left, right, top and bottom. If more fine-tuned control is desired, then a numeric vector of length 4 can be supplied to location, specifying the min x, max x, min y and max y values for the legend. See Examples.

Value

Invisibly returns a list with the following components:

coords A 2-column matrix of xy coordinates for each color bin in the legend.
width Coordinates for the short dimension of the legend.
pal The color ramp.
tickLocs The tick mark locations in plotting units.
labels The rate values associated with those tick locations.

Author(s)

Pascal Title

Examples

data(whales, events.whales)
ephy <- getEventData(whales, events.whales, burnin = 0.25, nsamples = 300)

# plot phylorate with extra margin space
x <- plot(ephy, lwd = 2, mar = c(5,4,4,4)) 
# presets
addBAMMlegend(x, location = 'topleft')
addBAMMlegend(x, location = 'bottom')
addBAMMlegend(x, location = 'right')

# fine-tune placement
x <- plot(ephy, lwd = 2, mar = c(5,4,4,4)) 
axis(1); axis(2)
addBAMMlegend(x, location = c(-1, -0.5, 40, 80), nTicks = 4)
addBAMMlegend(x, location = c(5, 20, 60, 61), nTicks = 4, side = 3,
              cex.axis = 0.7)

# addBAMMlegend also automatically detects the use of color.interval
data(primates, events.primates)
ephy <- getEventData(primates, events.primates, burnin=0.25,
                     nsamples = 300, type = 'trait')

x <- plot(ephy, breaksmethod = 'linear',
          color.interval = c(NA, 0.12), lwd = 2)
addBAMMlegend(x, location = c(0, 30, 200, 205), nTicks = 1, side = 3)

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.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'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/addBAMMlegend.Rd_%03d_medium.png", width=480, height=480)
> ### Name: addBAMMlegend
> ### Title: Add a color legend to a phylo-rate plot
> ### Aliases: addBAMMlegend
> 
> ### ** Examples
> 
> data(whales, events.whales)
> ephy <- getEventData(whales, events.whales, burnin = 0.25, nsamples = 300)
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  2495000
Analyzing  300  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> # plot phylorate with extra margin space
> x <- plot(ephy, lwd = 2, mar = c(5,4,4,4)) 
> # presets
> addBAMMlegend(x, location = 'topleft')
> addBAMMlegend(x, location = 'bottom')
> addBAMMlegend(x, location = 'right')
> 
> # fine-tune placement
> x <- plot(ephy, lwd = 2, mar = c(5,4,4,4)) 
> axis(1); axis(2)
> addBAMMlegend(x, location = c(-1, -0.5, 40, 80), nTicks = 4)
> addBAMMlegend(x, location = c(5, 20, 60, 61), nTicks = 4, side = 3,
+               cex.axis = 0.7)
> 
> # addBAMMlegend also automatically detects the use of color.interval
> data(primates, events.primates)
> ephy <- getEventData(primates, events.primates, burnin=0.25,
+                      nsamples = 300, type = 'trait')
Processing event data from data.frame

Discarded as burnin: GENERATIONS <  4990000
Analyzing  300  samples from posterior

Setting recursive sequence on tree...

Done with recursive sequence

> 
> x <- plot(ephy, breaksmethod = 'linear',
+           color.interval = c(NA, 0.12), lwd = 2)
> addBAMMlegend(x, location = c(0, 30, 200, 205), nTicks = 1, side = 3)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>