powerCalcPlot: Plotting PowerCalc Results

In LionelRohner/LRTools: A collection of functions written for analyzing Illumina HM450 and EPIC data

Description

Plotting function for powerCalc sample estimation. Generates a plot of the estimated sample size as a function of the CpG probes that have a power of 0.8.

Usage

powerCalcPlot(
  ...,
  sampleSizeSteps = c(5, 10, 15, 20, 25, 30, 35, 40, 45, 50),
  returnCleanPlotObj = FALSE,
  explicitNames = NULL
)

Arguments

...	Any data.frames produced by powerCalc.
sampleSizeSteps	Estimated sample sizes for which the number of CpG-probes with power of 0.8 are calculated. Represents the range that will be plotted. By default this is "c(5,10,15,20,25,30,35,40,45,50)".
returnCleanPlotObj	Returns an empty ggplot2 object that can be modified. Is set to "FALSE" by default.
explicitNames	The explicit names of the data.frames inputted in the dots argument. Maybe useful for plots shown in presentations. Assumes same order as the data.frames. Is not used by default.

Value

A plot or a ggplot object depending on returnCleanPlotObj choice.

Examples

# Standard Example

A <- data.frame(runif(1000,0.5,1),runif(1000,0.4,0.8),runif(1000,0.6,0.99),
                runif(1000,0.1,0.5),runif(1000,0.2,0.6),runif(1000,0,0.4))

colnames(A) <- rep(paste("Sample_",1:6,sep=""))
pdA <- data.frame(c(rep("Group_1",3),rep("Group_2",3)))
colnames(pdA) <- "Groups"

A <- as.matrix(A)

powerCalcA <-powerCalc(betaMatrix = A,
                       type = "unpaired",
                       pdGroups = pdA$Groups,
                       nameGroups = c("Group_1","Group_2"),
                       cutOff = 0.1)

B <- data.frame(runif(1000,0.8,1),runif(1000,0.8,0.9),runif(1000,0.7,0.9),
                runif(1000,0.05,0.3),runif(1000,0.2,0.3),runif(1000,0,0.3))

colnames(B) <- rep(paste("Sample_",1:6,sep=""))
pdB <- data.frame(c(rep("Group_1",3),rep("Group_2",3)))
colnames(pdB) <- "Groups"

B <- as.matrix(B)

powerCalcB <-powerCalc(betaMatrix = B,
                       type = "unpaired",
                       pdGroups = pdB$Groups,
                       nameGroups = c("Group_1","Group_2"),
                       cutOff = 0.1)

powerCalcPlot(powerCalcA, powerCalcB)

# Example with returnCleanPlotObj and explicitNames

g <- powerCalcPlot(powerCalcA, powerCalcB,
                   returnCleanPlotObj = TRUE,
                   explicitNames = c("I Am","The Greatest"))
library(ggplot2)
g + geom_line(aes(color = Group)) + labs(title = "my Title") # + etc as you like

LionelRohner/LRTools documentation built on Dec. 17, 2021, 1:10 a.m.