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Last data update: 2014.03.03

R: The plot method for a MDQC object

plot.mdqc

R Documentation

The plot method for a MDQC object

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 harringt@stat.ubc.ca and Gabriela V. Cohen Freue gcohen@stat.ubc.ca.

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.

Examples

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

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

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'demo()' for some demos, 'help()' for on-line help, or
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Type 'q()' to quit R.

> library(mdqc)
Loading required package: cluster
Loading required package: MASS
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/mdqc/plot.mdqc.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.mdqc
> ### Title: The plot method for a MDQC object
> ### Aliases: plot.mdqc
> ### Keywords: multivariate robust
> 
> ### ** Examples
> 
> data(allQC)
> mdout <- mdqc(allQC, method="cluster", k=3)
> plot(mdout)
> 
> ## Just one critical value
> plot(mdout, levels=0.9)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>