PlotPeptidesIdentified: Total number of peaks detected and sequenced
In BioAlvaro/ProteoMS: Quality Control of Protemics Data

Description Usage Arguments Value Examples

Total number of peaks detected and sequenced

PlotPeptidesIdentified(
  MQCombined,
  long_names = FALSE,
  sep_names = NULL,
  palette = "Set2"
)

`MQCombined`	Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`long_names`	If TRUE, samples having long names will be considered, and the name will be split by sep_names. By default = FALSE.
`sep_names`	If long_names is TRUE, sep_names has to be selected. Samples names will be split. By default is NULL.
`palette`	The palette from the Package RColorBrewer. By default is 'Set2'.

Plots the total number of unique peptide amino acid sequences identified from the recorded tandem mass spectra.

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MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics")
MQCombined <- make_MQCombined(MQPathCombined)
PlotPeptidesIdentified(MQCombined)