trypticHistogramLiP: Histogram of Half vs Fully tryptic peptides. Calculates...

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

Description

Histogram of Half vs Fully tryptic peptides. Calculates proteotypicity, and then uses calcualtions in histogram.

Usage

trypticHistogramLiP(
  data,
  fasta,
  x.axis.size = 10,
  y.axis.size = 10,
  legend.size = 10,
  width = 12,
  height = 4,
  color_scale = "bright",
  address = ""
)

Arguments

data	output of MSstatsLiP converter function. Must include at least ProteinName, PeptideSequence, BioReplicate, and Condition columns
fasta	A string of path to a FASTA file, used to match LiP peptides.
x.axis.size	size of x-axis labeling for plot. Default is 10.
y.axis.size	size of y-axis labeling for plot. Default is 10.
legend.size	size of feature legend for half vs fully tryptic peptides below graph. Default is 7.
width	Width of final pdf to be plotted
height	Height of final pdf to be plotted
color_scale	colors of bar chart. Must be one of "bright" or "grey". Default is "bright".
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 "TyrpticPlot.pdf". If address=FALSE, plot will be not saved as pdf file but shown in window..

Value

plot or pdf

Examples

# Use output of summarization function
trypticHistogramLiP(MSstatsLiP_Summarized,
                    system.file("extdata", "ExampleFastaFile.fasta", package="MSstatsLiP"),
                    color_scale = "bright", address = FALSE)

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