plot.genominator.goodness.of.fit: Create goodness-of-fit quantile-quantile plot

Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/goodnessOfFit.R

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

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## 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 [email protected], Kasper Daniel Hansen [email protected]

See Also

See Genominator vignette for more information. See also regionGoodnessOfFit.

Examples

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

Genominator documentation built on Nov. 1, 2018, 2:23 a.m.