View source: R/addBAMMlegend.R
addBAMMlegend | R Documentation |
Add a legend to a phylorate plot, with greater manual control.
addBAMMlegend( x, direction, side, location = "topleft", nTicks = 2, stretchInterval = FALSE, shortFrac = 0.02, longFrac = 0.3, axisOffset = 0.002, cex.axis = 0.8, labelDist = 0.7, ... )
x |
A |
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 |
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. |
stretchInterval |
If color.interval was defined, should the legend be stretched to the color.interval, or should the full range of rates be presented. |
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. |
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
.
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.
Pascal Title
Requires an object created with plot.bammdata
.
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)
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