oneGroupTwoLabelsCoMigration: Compare a Single Group of Proteins Between Two Label States

View source: R/oneGroupTwoLabelsCoMigration.R

oneGroupTwoLabelsCoMigrationR Documentation

Compare a Single Group of Proteins Between Two Label States

Description

This function creates a ?scatter plot? for a subset of proteins in dataFrame specified in groupData. Intended use of the function - using scenario A data, compare shape of the migration profile for a SINGLE GROUP of proteins BETWEEN the two LABEL STATES.

Usage

oneGroupTwoLabelsCoMigration(
  dataFrame,
  max_frac,
  groupData = NULL,
  groupName = "group1",
  meanLine = FALSE,
  medianLine = FALSE,
  ylabel = "Relative Protein Abundance",
  xlabel = "Fraction",
  legendLabel = "Condition",
  labelled = "Labeled",
  unlabelled = "Unlabeled",
  jitterPoints = 0.3,
  pointSize = 2.5,
  grid = FALSE,
  titleAlign = "left",
  alphaValue = 1,
  controlSample = "",
  textSize = 12,
  axisTextSize = 8
)

Arguments

dataFrame

dataFrame: data frame, data frame of normalised values for proteins from SCENARIO A, contains columns: 'Protein Group Accessions' character 'Protein Descriptions' character Fraction integer isLabel character ('TRUE'/'FALSE' values) 'Precursor Area' double scenario character

max_frac

numeric, total number of fractions

groupData

character vector, contins list of Protein Group Accessions that belong to the group we want to plot

groupName

character, name that should be used for the group specified in groupData

meanLine

logical, specifies whether to plot a mean line for all values in the group

medianLine

logical, specifies whether to plot a median line for all values in the group

ylabel

character

xlabel

character

legendLabel

character

labelled

character, label to be used for isLabel == TRUE

unlabelled

character, label to be used for isLabel == FALSE

jitterPoints

numeric

pointSize

numeric, size of the point in the plot

grid

logical, specifies presence/absence of gridline in the plot

titleAlign

character, one of the 'left', 'center'/'centre', 'right', specifies alignment of the title in plot

alphaValue

numeric, transparency of the point, values 0 to 1

controlSample

character, either labelled or unlabelled, this setting will adjust plot 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 normalised proteins file
inputFile <- system.file("extData", "dataNormProts.txt", package = "ComPrAn")
#read file in and change structure of table to required format
forAnalysis <- protImportForAnalysis(inputFile)
##example plot:
groupDV <- c("Q16540","P52815","P09001","Q13405","Q9H2W6")
groupName <- 'group1' 
max_frac <- 23 
oneGroupTwoLabelsCoMigration(forAnalysis, max_frac, groupDV,groupName)


Scavetta/ComPrAn documentation built on Oct. 3, 2022, 1:08 a.m.