plotRDIladder - RDI ladder plotting function

Description

function for adding a pre-computed RDI ladder onto a plot

Usage

plotRDIladder(ladder, side = 4, toPlot = NULL, labelLadder = TRUE,
add = TRUE, cex = 0.7, lineCol = NULL, fillCol = "#AAAAAA")

Arguments

ladder
the ladder object to add, as created by rdiLadder
side
integer; value between 1 and 4 indicating where the ladder will be added. 1 - bottom, 2 - left, 3 - top, 4 - right.
toPlot
logical vector; which ladders should be plotted? By default, ladders that are significantly overlapped by their neighbor and those that are majority outside the plotting region are removed.
labelLadder
logical; if TRUE, each curve will be annotated with the ladder name
add
logical; if TRUE, the ladder will be added to the current plot
cex
character expansion for ladder labels.
lineCol
the colors to be used for the ladder border. If the length of col is less than the length of ladder, col will be recycled.
fillCol
the colors to be used to fill the ladder. If the length of col is less than the length of ladder, col will be recycled.

Value

Invisibly returns the location of the ladder (if side 1 or 3, the y location; otherwise, the x location).

Details

This function is used in conjunction with rdiLadder to add a useful annotation to any plot containing RDI values.

Because RDI values vary according to the number of genes and size of the repertoires, they are not useful as numbers by themselves. Instead, it is useful to compare them with estimates of the true difference between the two repertoires. This function adds a series of density curves along one side of a standard plotting region, each one representing the most likely RDI values between two repertoires that vary by a set amount.

By default, not all density curves from the ladder parameter are plotted. Instead, the function intelligently chooses which ladders to plot based on the amount of overlap between neighboring ladders. If a ladder is significantly overlapped by the ladder below it, then the ladder will not be plotted. In addition, if the mean of a ladder is outside the main plotting region, it will be dropped. In order to control this behavior, you can directly specify which ladders are plotted using the toPlot parameter.

See also

rdiLadder, rdiModel, rdiAxis