PlotProteinsIdentified: Proteins Identified per sample.
In BioAlvaro/MQviewer: Quality Control of Protemics Data

Description Usage Arguments Value Examples

Proteins Identified per sample.

PlotProteinsIdentified(
  MQCombined,
  intensity_type = "Intensity",
  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`.
`intensity_type`	The type of intensity. Values: 'Intensity' or 'LFQ'. Only useful if split_violin_intensity = FALSE. Default is Intensity.
`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'.

A plot showing the number of proteins identified per sample and the number of missing values.

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