Usage
raPlot(a, b=NULL, uniques=5, normalize=FALSE,
nr=0, alpha = 0.01, jitter=FALSE, jit.wgts=NULL,
rex=1, flat=TRUE, tail=.5, arms=.5, spine=1, border=NULL, ...)Arguments
a
a vector of counts for a. can also be a matrix with two columns 1 for a and 2 for b.
b
a vector of counts for b.
uniques
a boolean specifying whether or not to plot the library-unique genes (those with zero counts in one or the other library).
normalize
A boolean specifying whether or not to normalize the counts into proportions.
nr
a numeric value indicating the asymptotic normalization ratio line.
alpha
a statisical significance value.
jitter
whether or not or how much to jitter the a and b counts into surrounding, non-overlapping space.
jit.wgts
a weight vector used to spread the counts of a and b into surrounding, non-overlapping space.
rex
a numeric value specifying the radial expansion of the plot points.
flat
a boolean for the radial expansion of points as a function of both R and A axes.
tail
a numeric or boolean value indicating the line thickness of the two trailing curved significance lines of the RAy.
arms
a numeric or boolean value indicating the line thickness of the two leading straight separator lines of the RAy.
spine
a numeric or boolean value indicating the line thickness of the normalization line (whose y position is specified by mm).
border
a vector of strings used to color the borders of the points.
...
other parameters passed to plot.