plotPaths: Plots MarkovJump paths for one taxon

In beast-dev/MarkovJumpR: Compute and plot Markov Jump inferences from BEAST

Description

Plots MarkovJump paths for one taxon

Usage

plotPaths(
  paths,
  locationMap = NULL,
  minTime = min(paths$startTime, paths$endTime),
  maxTime = max(paths$startTime, paths$endTime),
  defaultColor = "black",
  otherColor = "black",
  verticalColor = NULL,
  alpha = 0.1,
  yJitterSd = 0.1,
  cex.labels = 0.5,
  addLocationLine = FALSE,
  mustDisplayAllLocations = TRUE,
  xAt = NULL,
  xLabels = TRUE
)

Arguments

paths	MarkovJumps paths
locationMap	A locationMap object
minTime	Minimum time to plot
maxTime	Maximum time to plot
defaultColor	Default color for dwell times
otherColor	Color for locations not provided in locationMap
verticalColor	Color of transitions (default 'NULL' uses origin location color)
alpha	Alpha value to overlay dwell times
yJitterSd	Standard deviation of jitter around location
cex.labels	Location text label size
addLocationLine	Plot dashed line across locations
mustDisplayAllLocations	Check that locationMap contains all locations in paths
xAt	Time axis at values
xLabels	Time axis labels values

Value

MarkovJumps path object

beast-dev/MarkovJumpR documentation built on Sept. 17, 2020, 3:36 p.m.