PROPER (version 1.4.2)

plots: 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.

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)