plots {PROPER} | R Documentation |
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.
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)
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. |
Hao Wu <hao.wu@emory.edu>
comparePower
## 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)