plot.genominator.goodness.of.fit {Genominator} | R Documentation

## Create goodness-of-fit quantile-quantile plot

### Description

S3 method to plot `genominator.goodness.of.fit` object. Creates a quantile-quantile plot of the observed versus theoretical quantiles of goodness-of-fit statistics based on a chi-squared distribution.

### Usage

    ## S3 method for class 'genominator.goodness.of.fit'
    plot(x, chisq = FALSE, plotCol = TRUE,
      qqline = FALSE, xlab = "theoretical quantiles",
      ylab = "observed quantiles", main, pch = 16, cex = 0.75, ...)

### Arguments

`x` | An object of class `genominator.goodness.of.fit`, as returned by `regionGoodnessOfFit`.
`chisq` | Logical indicating whether chi-squared statistics should be plotted (as opposed to p-values from a chi-squared distribution).
`plotCol` | Logical indicating whether points at extreme quantiles should be colored.
`qqline` | Logical indicating whether a qqline should be added, this is a line through the 25%- and 75%-quantiles.
`xlab` | X-axis label for plot.
`ylab` | Y-axis label for plot.
`main` | Main label for plot.
`pch` | Plotting character type for plot.
`cex` | A numerical value giving the amount by which plotting text and symbols should be magnified relative to the default. See `par`.
`...` | Additional arguments for lower-level functions, namely `plot`.

### Details

This function constructs a quantile-quantile plot comparing the distribution of observed statistics to either the uniform 0,1 distribution or the appropriate chi-squared distribution. This plotting function provides a tool to assess whether replicate lanes, flow cells, sample preparations, etc. fit the model described in `regionGoodnessOfFit`.

### Value

This method is used for its side effect.

### Author(s)

James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu

### See Also

See `Genominator` vignette for more information. See also `regionGoodnessOfFit`.

### Examples

    ed <- ExpData(system.file(package = "Genominator", "sample.db"),
                  tablename = "raw")
    data("yeastAnno")
    plot(regionGoodnessOfFit(ed, yeastAnno), chisq = TRUE)

[Package Genominator version 1.40.0 Index]