MQ_evidence_modifications: Peptide modifications distribution using MaxQuant output

In tkostas/viewMQ: Visualization of MaxQuant output files for proteomics studies

Description

Uses the output from MaxQuant (evidence.txt) to create a bargraph of peptide modifications as a total or splitted by experiment.

Usage

MQ_evidence_modifications(x, per_sample = FALSE, ncol = 5,
  log_scale = TRUE)

Arguments

x	The filtered 'evidence.txt' file. Use MQ_remove_CR first to remove contaminants and reverse hits.
per_sample	Logical with default value equal to FALSE. By default a summary from all experiments will be plotted. If set to TRUE, individual experiments will be shown in different graphs.
ncol	Number of columns when plotting individual experiments. Default value is 5.
log_scale	Logical with default value equal to TRUE. By default, the y axis is in log10 scale. Set to FALSE to switch to normal scale.

Examples

# plot charge state as a total
MQ_evidence_modifications(filtered_evidence_output, per_sample = TRUE, ncol = 6)

#plot charge state per experiment
MQ_evidence_modifications(filtered_evidence_output, per_sample = TRUE, ncol = 6)

tkostas/viewMQ documentation built on May 6, 2019, 6:02 p.m.