ruv_rankplot {ruv}

RUV Rank Plot

Description

A plot showing the number of positive controls to be found within the N top-ranked features, as a function of N. The ranking of the features is by p-value.

Usage

ruv_rankplot(fit, pctl, X.col = "all", uniform.lines = 0)

Arguments

fit

The results of a call to ruv_summary.

pctl

Either an integer or character string specifying which column of fit$C to be used as positive controls. (Must be a logical vector). Alternatively, may some other index vector specifying the positive controls; importantly, in this case, the index vector must index the features as they are sorted in fit$C.

X.col

Which column of the X matrix to make the plot for. Can be either an integer or a character string. Or, if "all" (the default), use the F-test p-values.

uniform.lines

A vector of values between 0 and 1, or NULL. If specified, light gray lines will be drawn, showing (locally) uniform distributions.

Value

A ggplot.

Author(s)

Johann Gagnon-Bartsch