groupHeatMap: Make heatmap

View source: R/groupHeatMap.R

groupHeatMapR 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)


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