msmsEDA (version 1.10.0)

spc.densityplots: SpC density plots of a SpC matrix

Description

Draws superposed density plots, one for each column (sample) in a SpC matrix. The SpC are previosly transformed by log2, with an offset of 0.1. If a factor is provided the density curves are colored by factor level to better visualize the differences.

Usage

spc.densityplots(msms.counts,fact=NULL,minSpC=2,...)

Arguments

msms.counts

A SpC matrix with proteins in the rows and samples in the columns.

minSpC

All matrix cells with values below this threshold are excluded.

fact

NULL or a factor of length equal to the number of columns in the expression matrix. If provided the density curves are colored by factor level.

...

Extra parameters passed to the plot function.

Details

More informative plots are obtained when excluding the cells with values below 2, the default for minSpC.

Examples

data(msms.dataset)
spc.densityplots(exprs(msms.dataset),fact=pData(msms.dataset)[,1],
      main="UPS1 200fm vs 600fm")