plots {PROPER} | R Documentation

## Plot the stratified curves for power-related quantities

### Description

These are a group of functions to generate plot to visualize the stratified power metrics, including stratified power, FDR, true discoveries, false discoveries, false discovery cost, and type I error. There will be a line for each sample size. X-axis are strata and y-axis are the metrics. Error bars will be plotted if requested.

### Usage

    plotPower(powerOutput, cols = 1:ncol(powerOutput$FD),
        lty = 1:ncol(powerOutput$power), main = "", ylab = "Power",
        leg = TRUE, error.bar=TRUE)

    plotFDR(powerOutput, cols = 1:ncol(powerOutput$FDR), lty=1:ncol(powerOutput$FDR),
        main = "", ylab="FDR", leg = TRUE, error.bar=TRUE)

    plotPowerTD(powerOutput, cols = 1:ncol(powerOutput$TD),
        lty=1:ncol(powerOutput$TD), main="", ylab = "# True Discoveries",
        leg = TRUE, error.bar=TRUE)

    plotPowerFD(powerOutput, cols = 1:ncol(powerOutput$FD), lty=1:ncol(powerOutput$FD),
        main = "", ylab = "# False Discoverie", leg = TRUE, error.bar=TRUE)

    plotFDcost(powerOutput, cols = 1:ncol(powerOutput$FD), lty=1:ncol(powerOutput$FD),
        main="", ylab = "False discovery cost", leg = TRUE, error.bar=TRUE)

    plotPowerAlpha(powerOutput, cols = 1:ncol(powerOutput$alpha), lty=1:ncol(powerOutput$alpha),
        main = "", ylab = "False positive rate", leg = TRUE, error.bar=TRUE)

    plotAll(powerOutput)

### Arguments

`powerOutput` | Result object from "comparePower" function.
`cols, lty` | Colors and line types of the TD curves.
`main` | Figure title.
`ylab` | Y-axis label.
`leg` | Indicator for having figure legend or not.
`error.bar` | Indicator for whether plotting error bars in the figures.

### Author(s)

Hao Wu <hao.wu@emory.edu>

### See Also

comparePower

### Examples

    ## Not run:
    simOptions = RNAseq.SimOptions.2grp()
    ## run a few simulations
    simRes = runSims(Nreps=c(3,5,7), sim.opts=simOptions, nsims=5,
                     DEmethod="edgeR")

    ## using FDR 0.1 to call DE, then look at power curves and summary
    powers = comparePower(simRes)
    ## plot
    par(mfrow=c(2,3))
    plotPower(powers)
    plotPowerTD(powers)
    plotFDR(powers)
    plotFDcost(powers)
    plotPowerAlpha(powers)

    ## in one figure
    par(mfrow=c(2,3))
    plotAll(powers)

    ## End(Not run)

[Package PROPER version 1.20.0 Index]