PlotPTM: Post-Translational Modifications

Description Usage Arguments Value Examples

View source: R/PlotPTM.R

Description

Post-Translational Modifications

Usage

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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

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

BioAlvaro/MQviewer documentation built on Jan. 11, 2022, 8:25 p.m.