PlotPTM {MQmetrics} | R Documentation

## Post-Translational Modifications

### Description

Post-Translational Modifications

### Usage

    PlotPTM(
      MQCombined,
      peptides_modified = 1,
      plot_unmodified_peptides = FALSE,
      log_base = 2,
      aggregate_PTMs = TRUE,
      combine_same_residue_ptms = TRUE,
      palette = "Set2",
      plots_per_page = 5
    )

### Arguments

`MQCombined` | Object list containing all the files from the MaxQuant output. It is the result from using `make_MQCombined`.
`peptides_modified` | Minimum number of peptides modified. Default is 5.
`plot_unmodified_peptides` | If TRUE, it will show the Unmodified peptides.
`log_base` | The logarithmic scale for the intensity. Default is 2.
`aggregate_PTMs` | If TRUE, same PTM that occur multiple times in the same peptides, will be aggregated together.
`combine_same_residue_ptms` | Combine the PTMs that happen in the same residue such as Dimethyl (KR), Trimethyl (KR) into only one group: Methyl (KR).
`palette` | The palette from the Package RColorBrewer. By default is 'Set2'.
`plots_per_page` | Establish the maximum number of plots per page.

### Value

Two plots per sample

### Examples

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

[Package MQmetrics version 1.2.0 Index]