`R/Plots.R`

`plotExpectedType1Error.Rd`

`plotExpectedType1Error`

creates a plot showing the expected type 1 error as a function of standard error.

```
plotExpectedType1Error(
logRrNegatives,
seLogRrNegatives,
seLogRrPositives,
alpha = 0.05,
null = NULL,
xLabel = "Relative risk",
title,
showCis = FALSE,
showEffectSizes = FALSE,
fileName = NULL
)
```

- logRrNegatives
A numeric vector of effect estimates of the negative controls on the log scale.

- seLogRrNegatives
The standard error of the log of the effect estimates of the negative controls.

- seLogRrPositives
The standard error of the log of the effect estimates of the positive controls.

- alpha
The alpha (nominal type 1 error) to be used.

- null
An object representing the fitted null distribution as created by the

`fitNull`

function. If not provided, a null will be fitted before plotting.- xLabel
If showing effect sizes, what label should be used for the effect size axis?

- title
Optional: the main title for the plot

- showCis
Show 95 percent credible intervals for the expected type 1 error.

- showEffectSizes
Show the expected effect sizes alongside the expected type 1 error?

- fileName
Name of the file where the plot should be saved, for example 'plot.png'. See the function

`ggsave`

in the ggplot2 package for supported file formats.

A Ggplot object. Use the `ggsave`

function to save to file.

Creates a plot with the standard error on the x-axis and the expected type 1 error on the y-axis. The red line indicates the expected type 1 error given the estimated empirical null distribution if no calibration is performed. The dashed line indicated the nominal expected type 1 error rate, assuming the theoretical null distribution.

If standard errors are provided for non-negative estimates these will be plotted on the red line as yellow diamonds.

```
data(sccs)
negatives <- sccs[sccs$groundTruth == 0, ]
positive <- sccs[sccs$groundTruth == 1, ]
plotExpectedType1Error(negatives$logRr, negatives$seLogRr, positive$seLogRr)
```