counts.heatmap: Heatmap of an spectral counts matrix.
In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description Usage Arguments Details Value Author(s) See Also Examples

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

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

`msnset`	A MSnSet with spectral counts in the expression matrix.
`etit`	The root name of the pdf file names where the heatmaps are sent.
`fac`	A factor which is used for the column color bar.
`to.pdf`	A logical indicating whether the heatmaps are sent to a pdf file.

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.

No value is returned

Josep Gregori

MSnSet, heatmap and heatmap.2

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

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