Plots the genome

Description

Basic plot of the log2 ratios for each array ordered along the genome.

Usage

plotGenome(aCGH.obj, samples = 1:num.samples(aCGH.obj), naut = 22,
           Y = TRUE, X = TRUE, data = log2.ratios(aCGH.obj),
           chrominfo = human.chrom.info.Jul03,
           yScale = c(-2, 2), samplenames = sample.names(aCGH.obj),
           ylb = "Log2Ratio")

Arguments

See Also

aCGH

Examples

#plot samples in the order of descending quality 
data(colorectal)
order.quality <- order(sd.samples(colorectal)$madGenome)
pdf("plotGenome.orderByQuality.pdf")
par(mfrow=c(2,1))
for(i in order.quality)
   plotGenome(colorectal, samples = i, Y = FALSE)
dev.off()

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(aCGH)
Loading required package: cluster
Loading required package: survival
Loading required package: multtest
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")'.


Attaching package: 'aCGH'

The following object is masked from 'package:stats':

    heatmap

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/aCGH/plotGenome.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGenome
> ### Title: Plots the genome
> ### Aliases: plotGenome plotGene plotGeneSign maPalette plotCGH.func
> ### Keywords: hplot
> 
> ### ** Examples
> 
> 
> #plot samples in the order of descending quality 
> data(colorectal)
> order.quality <- order(sd.samples(colorectal)$madGenome)
> pdf("plotGenome.orderByQuality.pdf")
> par(mfrow=c(2,1))
> for(i in order.quality)
+    plotGenome(colorectal, samples = i, Y = FALSE)
> dev.off()
png 
  2 
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>