ResistanceBarcodePlotLiP: Proteolytic Resistance Barcode plot. Shows accessibility...

In Vitek-Lab/MSstatsLiP: LiP Significance Analysis in shotgun mass spectrometry-based proteomic experiments

Proteolytic Resistance Barcode plot. Shows accessibility score of different fully tryptic peptides in a protein.

Description

Proteolytic Resistance Barcode plot. Shows accessibility score of different fully tryptic peptides in a protein.

Usage

ResistanceBarcodePlotLiP(
  data,
  fasta_file,
  which.prot = "all",
  which.condition = "all",
  differential_analysis = FALSE,
  which.comp = "all",
  adj.pvalue.cutoff = 0.05,
  FC.cutoff = 0,
  width = 12,
  height = 4,
  address = ""
)

Arguments

data	list of data.tables containing LiP and TrP data in MSstatsLiP format. Should be output of summarization function as dataSummarizationLiP.
fasta_file	A string of path to a FASTA file
which.prot	a list of peptides to be visualized. Default is "all" which will plot a separate barcode plot for each protein.
which.condition	a list of conditions to be visualized. Default is "all" which will plot all conditions for a single protein in the same barcode plot.
differential_analysis	a boolean indicating if a barcode plot showing the differential analysis should be plotted. If this is selected you must have performed differential analysis on the proteoltic data in the calculateProteolyticResistance function. Default is FALSE.
which.comp	a list of comparisons to be visualized, if differential analysis is passed to plot_differential variable. Default is "all" which will plot a separate barcode plot for each comparison and protein.
adj.pvalue.cutoff	Default is .05. Alpha value for testing significance of model output.
FC.cutoff	Default is 0. Minimum absolute FC before a comparison will be considered significant.
width	width of the saved file. Default is 10.
height	height of the saved file. Default is 10.
address	the name of folder that will store the results. Default folder is the current working directory. The other assigned folder has to be existed under the current working directory. An output pdf file is automatically created with the default name of "VolcanoPlot.pdf" or "Heatmap.pdf". The command address can help to specify where to store the file as well as how to modify the beginning of the file name. If address=FALSE, plot will be not saved as pdf file but showed in window

Value

plot or pdf

Examples

# Specify Fasta path
fasta_path = system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP")

# Use model data to create Barcode Plot
#ResistanceBarcodePlotLiP(MSstatsLiP_model, fasta_path)

Vitek-Lab/MSstatsLiP documentation built on April 5, 2024, 3:25 a.m.