R: RDI ladder plotting function

plotRDIladder {rdi}

R Documentation

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.

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.

Value