twoGroupsWithinLabelCoMigration: Compare a Two Groups of Proteins Within One Label State

In Scavetta/complexomics: Complexome Profiling Analysis package

Compare a Two Groups of Proteins Within One Label State

Description

This function creates a scatter plot for a subset of proteins in dataFrame specified in group1Data and group2Data, label states are always separated into facets

Usage

twoGroupsWithinLabelCoMigration(
  dataFrame,
  max_frac,
  group1Data = NULL,
  group1Name = "group1",
  group2Data = NULL,
  group2Name = "group2",
  meanLine = FALSE,
  medianLine = FALSE,
  ylabel = "Relative Protein Abundance",
  xlabel = "Fraction",
  legendLabel = "Group",
  labelled = "Labeled",
  unlabelled = "Unlabeled",
  jitterPoints = 0.3,
  pointSize = 2.5,
  grid = FALSE,
  showTitle = FALSE,
  titleAlign = "left",
  alphaValue = 1,
  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
group1Data	character vector, contins list of Protein Group Accessions that belong to the group we want to plot for group 1
group1Name	character, name that should be used for the group specified in group1Data
group2Data	character vector, contins list of Protein Group Accessions that belong to the group we want to plot for group 2
group2Name	character, name that should be used for the group specified in group2Data
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
showTitle	logical
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
textSize	numeric, size of text in the plot
axisTextSize	numeric, size of axis labels in the plot

Details

Intended use of the function - using scenario A data, compare shape of the migration profile between a TWO GROUPS of proteins WITHIN the ONE LABEL STATE

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:
g1D <- c("Q16540","P52815","P09001","Q13405","Q9H2W6") #group 1 data vector
g1N <- 'group1'                                        #group 1 name
g2D <- c("Q9NVS2","Q9NWU5","Q9NX20","Q9NYK5","Q9NZE8") #group 2 data vector
g2N <- 'group2'                                        #group 2 name
max_frac <- 23 
twoGroupsWithinLabelCoMigration(forAnalysis, max_frac, g1D, g1N, g2D, g2N)

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