spc.boxplots: Set of SpC boxplots by sample

In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description

Draws a boxplot 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 boxplots are colored by factor level to better visualize the differences.

Usage

spc.boxplots(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 boxplots 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.

Author(s)

Josep Gregori

Examples

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

msmsEDA documentation built on Nov. 8, 2020, 6:55 p.m.