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Last data update: 2014.03.03

R: M vs. A Matrix

mva.pairs

R Documentation

M vs. A Matrix

Description

A matrix of M vs. A plots is produced. Plots are made on the upper triangle and the IQR of the Ms are displayed in the lower triangle

Usage

mva.pairs(x, labels=colnames(x), log.it=TRUE,span=2/3,family.loess="gaussian",
          digits=3,line.col=2,main="MVA plot",cex=2,...)

Arguments

`x`	a matrix containing the chip data in the columns.
`labels`	the names of the variables.
`log.it`	logical. If `TRUE`, uses log scale.
`span`	span to be used for loess fit.
`family.loess`	`"gaussian"` or `"symmetric"` as in `loess`.
`digits`	number of digits to use in the display of IQR.
`line.col`	color of the loess line.
`main`	an overall title for the plot.
`cex`	size for text.
`...`	graphical parameters can be given as arguments to `mva.plot`

.

See Also

pairs

Examples

    x <- matrix(rnorm(4000),1000,4)
    x[,1] <- x[,1]^2
    dimnames(x) <- list(NULL,c("chip 1","chip 2","chip 3","chip 4"))
    mva.pairs(x,log=FALSE,main="example")

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(affy)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/affy/mva.pairs.Rd_%03d_medium.png", width=480, height=480)
> ### Name: mva.pairs
> ### Title: M vs. A Matrix
> ### Aliases: mva.pairs
> ### Keywords: hplot
> 
> ### ** Examples
> 
>     x <- matrix(rnorm(4000),1000,4)
>     x[,1] <- x[,1]^2
>     dimnames(x) <- list(NULL,c("chip 1","chip 2","chip 3","chip 4"))
>     mva.pairs(x,log=FALSE,main="example")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>