plotCombination2genes: Plot a Combination of Two Genes

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Plot a Combination of Two Genes

Usage

plotCombination2genes(
  probesetId1 = NULL,
  probesetId2 = NULL,
  geneSymbol1 = NULL,
  geneSymbol2 = NULL,
  object,
  groups,
  addLegend = TRUE,
  legendPos = "topleft",
  probe2gene = TRUE,
  colvec = NULL,
  ...
)

Arguments

probesetId1	First probeset id, plotted in the x-axis
probesetId2	Second probeset id, plotted in the y-axis
geneSymbol1	First gene symbol, plotted in the x-axis
geneSymbol2	Second gene symbol, plotted in the y-axi
object	ExpressionSet object for the experiment
groups	string containing the name of the grouping variable
addLegend	Logical value to indicate whether a legend needs to be draw
legendPos	Position on the graph where to put the legend
probe2gene	should the probeset be translated to a gene symbol (used for the default title of the plot
colvec	a character vector of colors. If not specified it will be automatically generated by a4palette
...	This allows to specify typical arguments in the plot functio

Value

If a gene id is given, the plots for only the first probeset is displayed and a character vector of corresponding probeset IDs is returned invisibly. It is a list containing

probeset1	Probeset ids measuring 'gene1'
probeset1	Probeset ids measuring 'gene1'

If a probeset id is given, one single profile plot for the probeset is displayed.

Author(s)

W. Talloen, T. Verbeke

See Also

plot1gene

Examples

if (require(ALL)){
 data(ALL, package = "ALL")
 ALL <- addGeneInfo(ALL)
 aa <- plotCombination2genes(geneSymbol1 = 'HLA-DPB1', geneSymbol2 = 'CD3D',
		object = ALL, groups = "BT",
		addLegend = TRUE, legendPos = 'topright')
 aa
}

a4Base documentation built on Nov. 8, 2020, 5:41 p.m.