plot.genominator.goodness.of.fit {Genominator} | R Documentation |
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.
## 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, ...)
x |
An object of class |
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 |
... |
Additional arguments for lower-level functions, namely |
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
.
This method is used for its side effect.
James Bullard bullard@berkeley.edu, Kasper Daniel Hansen khansen@jhsph.edu
See Genominator
vignette for more information. See also regionGoodnessOfFit
.
ed <- ExpData(system.file(package = "Genominator", "sample.db"), tablename = "raw") data("yeastAnno") plot(regionGoodnessOfFit(ed, yeastAnno), chisq = TRUE)