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Last data update: 2014.03.03

R: Auxiliary functions to create Figures

affycomp.figures.auxiliary

R Documentation

Auxiliary functions to create Figures

Description

These functions are auxiliary function to affycompPlot. These Figures are used to assess an expression measure. They take components created by the assessDilution and assessSpikeIn functions.

Usage

affycomp.figure1(l,main="Figure 1",xlim=NULL,ylim=NULL)
affycomp.figure1b(l,main="Figure 1b",xlim=NULL,ylim=NULL,cex=0.85,all=FALSE)
affycomp.figure2(l,main="Figure 2")
affycomp.figure2b(l,main="Figure 2b")
affycomp.figure3(l, main = "Figure 3")
affycomp.figure4a(l, main = "Figure 4a",equal.lims=FALSE)
affycomp.figure4b(l, main = "Figure 4b")
affycomp.figure4c(l, rotate=TRUE, main = "Figure 4c")
affycomp.figure5a(l, main = "Figure 5a",maxfp=100)
affycomp.figure5b(l, main = "Figure 5b",maxfp=100)
affycomp.figure5c(l, main = "Figure 5c",maxfp=100)
affycomp.figure5d(l, main = "Figure 5d",maxfp=100)
affycomp.figure5e(l, main = "Figure 5e",maxfp=100)
affycomp.figure6a(l, main = "Figure 6a",xlim = NULL, ylim = NULL)
affycomp.figure6b(l, main = "Figure 6b",xlim = NULL, ylim = NULL)

Arguments

`l`	A list with the necessary components to create the Figure. See details.
`main`	Title for the Figure.
`maxfp`	range of the false positives in ROC will be from 0 to `maxfp`
`xlim`	x-axis limits.
`ylim`	y-axis limits.
`cex`	size of numbers in figure 1b.
`all`	logical. If `TRUE` all spikeins are shown. Otherwise, only those resulting in smaller, realistic, fold changes are shown.
`equal.lims`	logical. If `TRUE` the limits of x-axis and y-axis will have same range.
`rotate`	in the case of compfig4c one can eiher show the actual local slopes or the bias (local slope minus 1).

Details

Read the vignette for more details on what each Figure is. You can read assessSpikeIn and assessDilution to see which assessments are needed.

Value

Figures are produced.

Author(s)

Rafael A. Irizarry

Examples



library(affycompData)
data(rma.assessment)
affycomp.figure1(rma.assessment$MA)
affycomp.figure2(rma.assessment$Dilution)
affycomp.figure3(rma.assessment$Dilution)
affycomp.figure4a(rma.assessment$Signal)
affycomp.figure4b(rma.assessment$Dilution)
affycomp.figure5a(rma.assessment$FC)
affycomp.figure5b(rma.assessment$FC2)
affycomp.figure6a(rma.assessment$FC)
affycomp.figure6b(rma.assessment$FC)

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)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(affycomp)
Loading required package: Biobase
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

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/affycomp/affycomp.figures.auxiliary.Rd_%03d_medium.png", width=480, height=480)
> ### Name: affycomp.figures.auxiliary
> ### Title: Auxiliary functions to create Figures
> ### Aliases: affycomp.figures.auxiliary affycomp.figure1 affycomp.figure1b
> ###   affycomp.figure2 affycomp.figure2b affycomp.figure3 affycomp.figure4a
> ###   affycomp.figure4b affycomp.figure4c affycomp.figure5a
> ###   affycomp.figure5b affycomp.figure5c affycomp.figure5d
> ###   affycomp.figure5e affycomp.figure6a affycomp.figure6b
> ### Keywords: hplot
> 
> ### ** Examples
> 
> library(affycompData)
> data(rma.assessment)
> affycomp.figure1(rma.assessment$MA)
> affycomp.figure2(rma.assessment$Dilution)
> affycomp.figure3(rma.assessment$Dilution)
> affycomp.figure4a(rma.assessment$Signal)
> affycomp.figure4b(rma.assessment$Dilution)
> affycomp.figure5a(rma.assessment$FC)
> affycomp.figure5b(rma.assessment$FC2)
> affycomp.figure6a(rma.assessment$FC)
> affycomp.figure6b(rma.assessment$FC)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>