plot.mdqc: The plot method for a MDQC object

In mdqc: Mahalanobis Distance Quality Control for microarrays

Description

The plot method for a MDQC object, which plots ...

Usage

## S3 method for class 'mdqc'
plot(x, levels = c(0.9, 0.95, 0.99), xlab="", ylab="",
mfrow=NULL, mfcol=NULL, ...)

Arguments

x	An object of the class ‘mdqc’.
levels	A vector or scalar between 0 and 1 for displaying critical values for outliers. See details.
xlab	The label for for x-axis. Note that when there are multiple plots, the same value of this argument is used for each one.
ylab	The label for the y-axis. Note that when there are multiple plots, the same value of this argument is used for each one.
mfrow	Specify the arrangement of plots on the page, by rows, or leave NULL to let the function work it out
mfcol	As for mcol, but arrange plots by column instead
...	Other arguments passed to the default plot method.

Details

This plot method is for the output from the function mdqc, and plots the Mahalanobis distances for each array. The levels argument plots horizontal lines at critical values (based on the quantiles of a chi-squard distribution), and aids in identifying outliers.

For further details, see Cohen Freue et al. (2007)

Author(s)

Justin Harrington [e-mail] and Gabriela V. Cohen Freue [e-mail].

References

Cohen Freue, G. V. and Hollander, Z. and Shen, E. and Zamar, R. H. and Balshaw, R. and Scherer, A. and McManus, B. and Keown, P. and McMaster, W. R. and Ng, R. T. (2007) ‘MDQC: A New Quality Assessment Method for Microarrays Based on Quality Control Reports’. Bioinformatics 23, 3162 – 3169.

See Also

mdqc

Examples

data(allQC)
mdout <- mdqc(allQC, method="cluster", k=3)
plot(mdout)

## Just one critical value
plot(mdout, levels=0.9)

mdqc documentation built on Nov. 8, 2020, 11 p.m.