spc.scatterplot: Scatterplot of SpC means comparing two conditions
In msmsEDA: Exploratory Data Analysis of LC-MS/MS data by spectral counts

Description Usage Arguments Details Author(s) Examples

Given a SpC matrix and a two levels factor, draws a scatterplot with SpC means of one condition in the x axis and SpC means of the second condition in the y axis.

1	spc.scatterplot(msms.counts, treat, trans="log2", minSpC=2, minLFC=1, ...)

`msms.counts`	A SpC matrix with proteins in the rows and samples in the columns.
`treat`	A two level factor of length equal to the number of columns in the expression matrix. The two levels represent the conditions to be compared.
`trans`	The transformation made on the means before plotting. One among "log2", "sqrt", or "none". The default is "log2".
`minSpC`	Used as signal threshold.
`minLFC`	Used as size effect threshold.
`...`	Extra parameters passed to the plot function.

The transformed means are plotted, one condition versus the other. The borders representing absolute log fold change 1 are drawn as dashed lines. All features with log fold change equal to or greather than minLFC and with mean SpC in the most abundant condition equal to or greather than minSpC are colored in red.

Josep Gregori

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data(msms.dataset)
spc.scatterplot(exprs(msms.dataset),treat=pData(msms.dataset)[,1],trans="log2",
       minSpC=2,minLFC=1,main="UPS1 200fm vs 600fm")