Draw a coverage heatmap

Description

This method draws a heatmap of the coverage values using the matrix that is passed as an argument to the method

Usage

  ## S4 method for signature 'matrix'
draw.heatmap(data,outfile, color,...)
  ## S4 method for signature 'list'
draw.heatmap(data,outfile, color,...)

Arguments

Details

This function is used to create a coverage heatmap of the matrix/list of matrices generated using the cov.matrix function

Author(s)

Ernesto Lowy <ernestolowy@gmail.com>

See Also

cov.matrix

Examples

  ## draw the heatmap for a coverate matrix that was previously calculated 
  # using the cov.matrix function for a BAM file containing ChIP-seq data 
  # from a H3K36me3 histone modification experiment
  data(DF_H3K36me3)
  draw.heatmap(DF_H3K36me3,outfile="testHeatmap.png")
  
  ## Now, draw two heatmaps for 2 different coverage matrices previously 
  # obtained for the same H3K36me3 histone modification experiment and its
  # respective 'control' file
  data(DF_H3K36me3_control)
  
  # create a list with the two matrices
  input_l=list(DF_H3K36me3,DF_H3K36me3_control)
  draw.heatmap(input_l,outfile="testHeatmap.png")

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(CoverageView)
Loading required package: Rsamtools
Loading required package: GenomeInfoDb
Loading required package: stats4
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

Attaching package: 'S4Vectors'

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

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: Biostrings
Loading required package: XVector
Loading required package: rtracklayer

Attaching package: 'CoverageView'

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

    export.wig

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/CoverageView/draw.heatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: draw.heatmap
> ### Title: Draw a coverage heatmap
> ### Aliases: draw.heatmap draw.heatmap,matrix-method
> ###   draw.heatmap,list-method
> 
> ### ** Examples
> 
>   ## draw the heatmap for a coverate matrix that was previously calculated 
>   # using the cov.matrix function for a BAM file containing ChIP-seq data 
>   # from a H3K36me3 histone modification experiment
>   data(DF_H3K36me3)
>   draw.heatmap(DF_H3K36me3,outfile="testHeatmap.png")
png 
  2 
>   
>   ## Now, draw two heatmaps for 2 different coverage matrices previously 
>   # obtained for the same H3K36me3 histone modification experiment and its
>   # respective 'control' file
>   data(DF_H3K36me3_control)
>   
>   # create a list with the two matrices
>   input_l=list(DF_H3K36me3,DF_H3K36me3_control)
>   draw.heatmap(input_l,outfile="testHeatmap.png")
png 
  2 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>