oneGroupTwoLabelsCoMigration {ComPrAn} | R 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)

[Package ComPrAn version 1.2.0 Index]