PlotPTM {MQmetrics} | R Documentation |
Post-Translational Modifications
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 )
MQCombined |
Object list containing all the files from the MaxQuant
output. It is the result from using |
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. |
Two plots per sample
MQPathCombined <- system.file("extdata/combined/", package = "MQmetrics") MQCombined <- make_MQCombined(MQPathCombined) PlotPTM(MQCombined)