trypticHistogramLiP {MSstatsLiP} | R Documentation

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

### 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)

[Package MSstatsLiP version 1.0.0 Index]