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

Description Usage Arguments Value Examples

View source: R/trypticHistogramLiP.R

Description

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

Usage

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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

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# 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.