groupHeatMap: Make heatmap

In Scavetta/complexomics: Complexome Profiling Analysis package

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)

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