Usage
# S3 method for partitionedRAD
plot(x,
fileprefix = NULL,
lnL.break = NULL,
regression = NULL,
ci = NULL,
widthScalar = .85,
panels = c('bestMat', 'worstMat', 'doubleCountMat'),
squareSize = switch(as.character(length(panels)), '2' = 5, '3' = 3),
primeTreeColor = 'red',
primeTreeCharacter = 19,
highlight.points = NULL,
highlight.colors = NULL,
filebase = 'DEFAULT',
...)Arguments
x
an object of class partitionedRAD
fileprefix
prefix of the files to save; as written, you have to provide some prefix
to identify the files if you want a pdf, but the remainder of the file name
defaults to a combination of parameters and date
lnL.break
a numeric vector, which should be the length of panels;
if not null, the lowest tree likelihood to show on each panel
regression
a boolean vector, which should be the length of panels;
if not null, whether to draw a linear fit line on each panel
ci
a numeric vector, the length of panels;
what CI to show on each regression, or 0 for no CI
widthScalar
a multiplier on the width of the entire plot to get the plotting panels square
or not as you prefer
panels
a character vector describing the order of panels;
can be any of "bestMat", "worstMat", "doubleCountMat" in any order
squareSize
the size of the panels in inches; defaults to 5" for a 2-panel plot,
3" for a 3-panel plot, only because that works well in my trials
primeTreeColor
the color of the dot representing the first tree in the matrix, which
should be your original tree (unpermuted) if you've been following the
workflow from genTrees through this final and exciting plot
primeTreeCharacter
the character of the dot representing the first tree in the matrix
highlight.points
number of any trees to highlight
highlight.colors
colors vector or single color for highlighted points
filebase
the base of the file name for exported plots
…
additional arguments passed to plot and rank.partitionedRAD