allPeptidesPlot: Create scatter plot

In Scavetta/complexomics: Complexome Profiling Analysis package

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")

Scavetta/complexomics documentation built on Oct. 1, 2022, 2:15 a.m.