sequence_plot: Plot the Sequence with Matched Fragments Annotations, split...

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

Plot the Sequence with Matched Fragments Annotations, split by a,b,c and x,y,z annotations

Description

A static plot with the sequence annotated with the lowest ppm error fragment per N-terminus (a, b, c) and C-terminus (x, y, z) fragment

Usage

sequence_plot(
  MatchedPeaks,
  IncludeIsotopes = FALSE,
  RemoveChargeAnnotation = FALSE,
  RemoveModification = FALSE,
  WrapLength = 8,
  LabelSize = 3
)

Arguments

MatchedPeaks	A matched_peaks object generated by get_matched_peaks. Required.
IncludeIsotopes	A logical to indicate whether isotopes should be included. Default is FALSE.
RemoveChargeAnnotation	A logical to indicate whether the annotation for charge states should be included in the plot. This does not remove charge states; rather, the annotation for charge states. Default is FALSE.
RemoveModification	A logical to indicate whether the modification on the residue should be removed in the plot. Default is FALSE.
WrapLength	An integer to index how many letters should be printed before wrapping. Default is 10, but the value will vary depending on the size of your visualization.
LabelSize	The size of the PTM labels. Default is 3.

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)
BU_Match2 <- get_matched_peaks(ScanMetadata = BU_ScanMetadata, PeakData = BU_Peak, AlternativeSequence = "IGA[Acetyl]VGGTENVSLTQSQMPAHNHLVAASTVSGTVKPLANDIIGAGLNK")

# Make plots
sequence_plot(MatchedPeaks = BU_Match)
sequence_plot(MatchedPeaks = BU_Match, RemoveChargeAnnotation = TRUE)
sequence_plot(MatchedPeaks = BU_Match2)



## End(Not run)

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