Heatmap of an spectral counts matrix.

Description

Heatmap showing the clustering of proteins and samples in a matrix of spectral counts

Usage

counts.heatmap(msnset,etit=NULL,fac=NULL,to.pdf=FALSE)

Arguments

Details

A heatmap of the msnset expression matrix is plot. If to.pdf is TRUE two heatmaps are plot, the first is fitted on an A4 page, the second is plotted with 3mm by row, allocating enough height to make the rownames readable. If fac is not NULL then a column color bar will show the levels of the factor. If to.pdf is TRUE the heatmaps are sent to pdf files whose names are the concatenation of etit and "-HeatMap.pdf" and "-FullHeatMap.pdf", otherwise etit has no effect.

Value

No value is returned

Author(s)

Josep Gregori

See Also

MSnSet, heatmap and heatmap.2

Examples

data(msms.dataset)
msnset <- pp.msms.data(msms.dataset)
counts.heatmap(msnset,fac = pData(msnset)$treat)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(msmsEDA)
Loading required package: MSnbase
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")'.

Loading required package: mzR
Loading required package: Rcpp
Loading required package: BiocParallel
Loading required package: ProtGenerics

This is MSnbase version 1.20.7 
  Read '?MSnbase' and references therein for information
  about the package and how to get started.


Attaching package: 'MSnbase'

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

    smooth

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

    trimws

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/msmsEDA/counts.heatmap.Rd_%03d_medium.png", width=480, height=480)
> ### Name: counts.heatmap
> ### Title: Heatmap of an spectral counts matrix.
> ### Aliases: counts.heatmap
> ### Keywords: hplot multivariate
> 
> ### ** Examples
> 
> data(msms.dataset)
> msnset <- pp.msms.data(msms.dataset)
> counts.heatmap(msnset,fac = pData(msnset)$treat)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>