twoGroupsWithinLabelCoMigration {ComPrAn} | R 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)

[Package ComPrAn version 1.2.0 Index]