profilesPlot {a4Base} | R Documentation |
Plot expression profiles of multiple genes or probesets Plot expression profiles of multiple genes or probesets. Each line depicts a gene, and the color legend can be used to identify the gene.
profilesPlot( object, probesetIds, sampleIDs = TRUE, addLegend = TRUE, legendPos = "topleft", colvec = NULL, orderGroups = NULL, ... )
object |
ExpressionSet object for the experiment |
probesetIds |
The probeset ID. These should be stored in the |
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 |
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 |
colvec |
Vector of colors to be used for the groups. If not specified, the default colors of
|
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 |
... |
Possibility to add extra plot options. See |
No returned value, a plot is drawn in the current device.
W. Talloen
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") }