annotated_spectrum_plot: Annotate a Spectrum with Fragments

In EMSL-Computing/pspecterlib: PSpecteR Library - Visualization tools for top-down and bottom-up proteomics data

Annotate a Spectrum with Fragments

Description

Generates an experimental spectrum with calculated peptide fragments. Plot can be interactive or not.

Usage

annotated_spectrum_plot(
  PeakData,
  MatchedPeaks = NULL,
  IncludeIsotopes = TRUE,
  IncludeLabels = TRUE,
  LabelSize = 4,
  LabelDistance = 0.5,
  Interactive = FALSE
)

Arguments

PeakData	Object of the peak_data class from get_peak_data.
MatchedPeaks	Object of the matched_peaks class from get_matched_peaks. Default is NULL.
IncludeIsotopes	A logical to indicate whether isotopes should be included in the plot. Default is TRUE.
IncludeLabels	A logical to indicate whether labels should be included in the plot. Default is TRUE.
LabelSize	A numeric indicating the size of the label in ggplot dimensions. Default is 4.
LabelDistance	A numeric indicating the distance from each peak the label should be. Default is 0.5 M/Z.
Interactive	A logical to determine whether the plot should be interactive or not. For plots with more than 10,000 peaks, it is advantageous to set to FALSE. Default is TRUE.

Examples

## Not run: 

# Test bottom up data
BU_Peak <- get_peak_data(ScanMetadata = BU_ScanMetadata, ScanNumber = 31728)
BU_Match <- get_matched_peaks(ScanMetadata = BU_ScanMetadata, PeakData = BU_Peak)

annotated_spectrum_plot(PeakData = BU_Peak, Interactive = TRUE)
annotated_spectrum_plot(PeakData = BU_Peak, MatchedPeaks = BU_Match, IncludeLabels = FALSE, Interactive = TRUE)
annotated_spectrum_plot(PeakData = BU_Peak, MatchedPeaks = BU_Match, IncludeLabels = TRUE)

## End(Not run)

EMSL-Computing/pspecterlib documentation built on Jan. 28, 2024, 8:13 p.m.