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

View source: R/twoGroupsWithinLabelCoMigration.R

twoGroupsWithinLabelCoMigrationR Documentation

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