a4 (version 1.20.0)

plotCombination2genes: Plot a Combination of Two Genes

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-axis

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 drawn.

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 function

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.

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
}