allPeptidesPlot {ComPrAn} | R Documentation

## Create scatter plot

### Description

This function creates a plot of all peptides that belong to a single protein

### Usage

    allPeptidesPlot(
      .listDF,
      protein,
      max_frac,
      meanLine = FALSE,
      repPepLine = FALSE,
      separateLabStates = FALSE,
      grid = TRUE,
      titleLabel = "all",
      titleAlign = "left",
      ylabel = "Precursor Area",
      xlabel = "Fraction",
      legendLabel = "Condition",
      labelled = "Labeled",
      unlabelled = "Unlabeled",
      controlSample = "",
      textSize = 12,
      axisTextSize = 8
    )

### Arguments

`.listDF` | list, list containing data frames of peptides for each protein indexed by 'Protein Group Accessions'
`protein` | character, 'Protein Group Accession' to show in the plot
`max_frac` | numeric, total number of fractions
`meanLine` | logical, specifies whether to plot a mean line
`repPepLine` | logical, specifies whether to plot a representative peptide line
`separateLabStates` | logical, specifies whether label states will be separated into facets
`grid` | logical, specifies presence/absence of gridline in the plot
`titleLabel` | character, what to call the plot
`titleAlign` | character, one of the 'left', 'center'/'centre', 'right', specifies alignment of the title in plot
`ylabel` | character
`xlabel` | character
`legendLabel` | character
`labelled` | character, label to be used for isLabel == TRUE
`unlabelled` | character, label to be used for isLabel == FALSE
`controlSample` | character, either labelled or unlabelled, this setting will adjust coloring based on which sample is a control
`textSize` | numeric, size of text in the plot
`axisTextSize` | numeric, size of axis labels in the plot

### Value

plot

### Examples

    ##Use example peptide data set, read in and clean data
    inputFile <- system.file("extData", "data.txt", package = "ComPrAn")
    peptides <- peptideImport(inputFile)
    peptides <- cleanData(peptides, fCol = "Search ID")
    ## separate chemical modifications and labelling into separate columns
    peptides <- splitModLab(peptides)
    ## remove unneccessary columns, simplify rows
    peptides <- simplifyProteins(peptides)
    ## Pick representative peptide for each protein for both scenarios
    peptide_index <- pickPeptide(peptides)

    ##create a plot showing all peptides of selected protein
    protein <- "P52815"
    max_frac <- 23
    #default plot
    allPeptidesPlot(peptide_index,protein, max_frac = max_frac)
    #other plot version
    allPeptidesPlot(peptide_index,protein, max_frac = max_frac,
    repPepLine = TRUE, grid = FALSE, titleAlign = "center")
    #other plot version
    allPeptidesPlot(peptide_index,protein, max_frac = max_frac,
    repPepLine = TRUE, meanLine = TRUE, separateLabStates =TRUE,
    titleLabel = "GN")

[Package ComPrAn version 1.2.0 Index]