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Last data update: 2014.03.03

R: Visualize ChIP intensities along the chromosome

chipAlongChrom

R Documentation

Visualize ChIP intensities along the chromosome

Description

This function can visualize the array intensities from a ChIP chip experiment for a chromosomal region or the whole chromosome. It's based on the plotAlongChrom function from the package tilingArray, but provides a different visualization.

Usage

## S4 method for signature 'ExpressionSet,probeAnno'
plot(x, y, ...)

chipAlongChrom(eSet,  probeAnno, chrom, xlim, ylim, 
 samples = NULL, paletteName = "Set2", colPal = NULL,
 ylab = "Fold change [log]", ipch = 16, ilwd = 3, ilty = 1,
 icex = 3, gff = NULL,
 featureExclude=c("chromosome", "nucleotide_match","insertion"),
 zeroLine = TRUE, sampleLegend = TRUE, sampleLegendPos = "topleft",
 featureLegend = FALSE, maxInterDistance = 200,  coord = NULL,
 highlight, main, ...)

Arguments

`eSet`	An expression set containing the (normalized) ChIP intensities, e.g. the result objects from functions `preprocess` and `computeRunningMedians`.
`x`	Corresponds to argument `eSet` when calling the S4 method
`probeAnno`	An object of class `probeAnno` holding genomic position, index and gene association of probes on array.
`y`	Corresponds to argument `probeAnno` when calling the S4 method
`chrom`	character; the chromosome to visualize
`xlim`	start and end genomic coordinates on the chromosome to visualize
`ylim`	minimum and maximum probe intensities for the plot, if missing (default) set to `range(exprs(eSet))`
`samples`	numeric; which samples from the `eSet` are to be shown. Default is to show all samples in the `eSet`,
`paletteName`	character; Name of the RColorBrewer palette to use for sample colors. If the number of samples is greater than the palette size, random colors are taken.
`colPal`	vector of colors to use for the sample intensities. This is alternative to the argument `paletteName` for specifying which colors to use.
`ylab`	character; label for the y-axis, passed on to the plotting function as `ylab`
`ipch`	plot character to use
`icex`	character expansion to use for plotting symbol
`ilwd`	line width of plotted data lines
`ilty`	line type of plotted data lines; passed on to `par(lty)`.
`gff`	data frame containing annotation for genomic feature to be used to further annotate the plot.
`featureExclude`	character vector specifying the feature types in the data.frame `gff` that should not be shown in the plot
`zeroLine`	logical; should a dashed horizontal line at y=0 be put into the plot?
`sampleLegend`	logical; should a sample legend be put into the plot?
`sampleLegendPos`	character; where to put the sample legend; one of ‘topleft’ (default), ‘bottomleft’, ‘topright’, or ‘bottomrigth’
`featureLegend`	logical; should a feature legend be put beneath the plot?
`maxInterDistance`	numeric; only used when `itype` is either "r" or "u"; specifies the maximal distance up to which adjacent probe positions should be connected by a line.
`coord`	optional integer of length 2; can be used instead of `xlim` to specify the start and end coordinates of the genomic region to plot
`highlight`	optional list specifying a genomic region to be highlighted in the shown plot
`main`	optional main title for the plot; if not specified: the default is ‘Chromosome coordinate [bp]’
`...`	further parameters passed on to `grid.polyline` and `grid.points`

Value

invisible list of probe positions (element x) and probe levels (element y) in the selected genomic region.

Note

The S4 method is provided as a mere convenience wrapper.

When plotting a new ‘grid’ plot in an active x11 window that already contains a plot, remember to call grid.newpage() before.

Author(s)

Joern Toedling

Examples

  ### load data
  ringoExampleDir <- system.file("exData",package="Ringo")
  load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
  load(file.path(ringoExampleDir,"exampleX.rda"))

  ### show a gene that is well represented on this microarray
  plot(exampleX, exProbeAnno, chrom="9",
       xlim=c(34318000,34321000), ylim=c(-2,4), gff=exGFF)

  ### this should give you the same result as:
  chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
                 ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)

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(Ringo)
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")'.

Loading required package: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Ringo/chipAlongChrom.Rd_%03d_medium.png", width=480, height=480)
> ### Name: chipAlongChrom
> ### Title: Visualize ChIP intensities along the chromosome
> ### Aliases: chipAlongChrom plot,ExpressionSet,probeAnno-method
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   ### load data
>   ringoExampleDir <- system.file("exData",package="Ringo")
>   load(file.path(ringoExampleDir,"exampleProbeAnno.rda"))
>   load(file.path(ringoExampleDir,"exampleX.rda"))
> 
>   ### show a gene that is well represented on this microarray
>   plot(exampleX, exProbeAnno, chrom="9",
+        xlim=c(34318000,34321000), ylim=c(-2,4), gff=exGFF)
> 
>   ### this should give you the same result as:
>   chipAlongChrom(exampleX, chrom="9", xlim=c(34318000,34321000),
+                  ylim=c(-2,4), probeAnno=exProbeAnno, gff=exGFF)
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>