BarcodePlotLiP: Barcode plot. Shows protein coverge of LiP modified peptides.

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

Description

Barcode plot. Shows protein coverge of LiP modified peptides.

Usage

BarcodePlotLiP(
  data,
  fasta,
  model_type = "Adjusted",
  which.prot = "all",
  which.comp = "all",
  adj.pvalue.cutoff = 0.05,
  FC.cutoff = 0,
  FT.only = FALSE,
  width = 12,
  height = 4,
  address = ""
)

Arguments

data	list of data.tables containing LiP and TrP data in MSstatsLiP format. Should be output of modeling function such as groupComparisonLiP.
fasta	A string of path to a FASTA file
model_type	A string of either "Adjusted" or "Unadjusted", indicating whether to plot the adjusted or unadjusted models. Default is "Adjusted".
which.prot	a list of peptides to be visualized. Default is "all" which will plot a separate barcode plot for each protein.
which.comp	a list of comparisons to be visualized. Default is "all" which will plot a separate barcode plot for each condition and protein.
adj.pvalue.cutoff	Defualt 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.
FT.only	FALSE plots all FT and HT peptides, TRUE plots FT peptides only. Default is FALSE.
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
BarcodePlotLiP(MSstatsLiP_model, fasta_path,
              model_type = "Adjusted",
              address=FALSE)

devonjkohler/MSstatsLiP documentation built on Dec. 19, 2021, 11:01 p.m.