a4 (version 1.20.0)

profilesPlot: Plot expression profiles of multiple genes or probesets

Description

Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene.

Usage

profilesPlot(object, probesetIds, sampleIDs = TRUE, addLegend = TRUE, legendPos = "topleft", colvec = NULL, orderGroups = NULL, ...)

Arguments

object

ExpressionSet object for the experiment

probesetIds

The probeset ID. These should be stored in the featureNames of the expressionSet object.

colvec

Vector of colors to be used for the groups. If not specified, the default colors of a4palette are used.

sampleIDs

A boolean or a string to determine the labels on the x-axis. Setting it to FALSE results in no labels (interesting when the labels are unreadable due to large sample sizes). Setting it to a string will put the values of that particular pData column as labels. The string should be a name of a column in the pData of the expressionSet object."

addLegend

Boolean indicating whether a legend for the colors of the dots should be added.

legendPos

Specify where the legend should be placed. Typically either topright, bottomright, topleft (the default) or bottomleft

orderGroups

String containing the name of the grouping variable to order the samples in the x-axis accordingly. This should be a name of a column in the pData of the expressionSet object.

...

Possibility to add extra plot options. See par

See Also

plot1gene, boxPlot

Examples

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
  
  myGeneSymbol <- c("LCK")	# a gene 
  probesetPos <- which(myGeneSymbol == featureData(ALL)$SYMBOL)
  myProbesetIds <- featureNames(ALL)[probesetPos]
  
  profilesPlot(object = ALL, probesetIds = myProbesetIds, 
      orderGroups = "BT", sampleIDs = "BT")
}