Draw a heatmap-like multi-scale contact profile

Description

This method draws a fragment-based heatmap-like plot for 4C-seq data around a given viewpoint. For a given number of bands, color-coded running medians or running means of signal intensity (normalized and log-scaled) in different fragments are displayed; the window size of the running medians or running means increases from top to bottom. A corresponding colour legend is added in an extra plot.

Usage

  ## S4 method for signature 'Data4Cseq'
drawHeatmap(expData, plotFileName = "", smoothingType = "median", picDim = c(9, 2.2), bands = 5, cutoffLog = -7.0, xAxisIntervalLength = 50000, legendLabels = expression(2^-7, 2^0), useFragEnds = TRUE)
  ## S4 method for signature 'data.frame'
drawHeatmap(expData, plotFileName = "", smoothingType = "median", picDim = c(9, 2.2), bands = 5, cutoffLog = -7.0, xAxisIntervalLength = 50000, legendLabels = expression(2^-7, 2^0), useFragEnds = TRUE)

Arguments

Value

A multiscale intensity contact profile plot and a corresponding colour legend)

Note

PDF export and output as TIFF format are supported. The export format is chosen depending on the plot file name's ending. If no plot file name is provided, the result is plotted on screen.

Author(s)

Carolin Walter

Examples

  if(interactive()) {
    data(liverData)
    drawHeatmap(liverData)
  }

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(Basic4Cseq)
Loading required package: Biostrings
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: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
Loading required package: GenomicAlignments
Loading required package: GenomeInfoDb
Loading required package: GenomicRanges
Loading required package: SummarizedExperiment
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")'.

Loading required package: Rsamtools
Loading required package: caTools

Attaching package: 'caTools'

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

    runmean

The following object is masked from 'package:S4Vectors':

    runmean

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Basic4Cseq/drawHeatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: drawHeatmap
> ### Title: Draw a heatmap-like multi-scale contact profile
> ### Aliases: drawHeatmap drawHeatmap,Data4Cseq-method
> ###   drawHeatmap,data.frame-method
> ### Keywords: drawHeatmap
> 
> ### ** Examples
> 
> #  if(interactive()) {
>     data(liverData)
>     drawHeatmap(liverData)
> #  }
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>