groupHeatMap {ComPrAn} | R Documentation

## Make heatmap

### Description

This function creates a heatmap for a subset of proteins in dataFrame specified in groupData, heatmap is divided into facets according to isLabel

### Usage

    groupHeatMap(
      dataFrame,
      groupData,
      groupName,
      titleAlign = "left",
      newNamesCol = NULL,
      colNumber = 2,
      ylabel = "Protein",
      xlabel = "Fraction",
      legendLabel = "Relative Protein Abundance",
      legendPosition = "right",
      grid = TRUE,
      labelled = "labeled",
      unlabelled = "unlabeled",
      orderColumn = NULL
    )

### Arguments

`dataFrame` | data frame, contains columns: 'Protein Group Accessions' character 'Protein Descriptions' character Fraction integer isLabel character ('TRUE'/'FALSE' values) 'Precursor Area' double scenario character
`groupData` | data frame, mandatory column: 'Protein Group Accessions' character - this column is used for filtering optional columns: any other column of type character that should be used for renaming
`groupName` | character, name that should be used for the group specified in groupData
`titleAlign` | character, one of the 'left', 'center'/'centre', 'right', specifies alignment of the title in plot
`newNamesCol` | character, if groupData contains column for re-naming and you want to use it, specify the column name in here
`colNumber` | numeric, values of 1 or 2, specifies whether facets will be shown side-by-side or above each other
`ylabel` | character
`xlabel` | character
`legendLabel` | character
`legendPosition` | character, one of "right" or "bottom"
`grid` | logical, specifies presence/absence of gridline in the plot
`labelled` | character, label to be used for isLabel == TRUE
`unlabelled` | character, label to be used for isLabel == FALSE
`orderColumn` | character, if groupData contains column for re-ordering and you want to use it, specify the column name in here

### 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:
    groupDfn <- system.file("extData", "exampleGroup.txt", package = "ComPrAn")
    groupName <- 'group1'
    groupData <- data.table::fread(groupDfn)
    groupHeatMap(forAnalysis[forAnalysis$scenario == "B",], groupData, groupName)

[Package ComPrAn version 1.2.0 Index]