boxPlot: Create a boxplot for a given gene.

In a4Base: Automated Affymetrix Array Analysis Base Package

Description

Create a boxplot for a given gene. The boxplot displays the expression values (y-axis) by groupss (x-axis). The raw data are superimposed as dots, jittered for readability of the plot. Optionally, the dots can be colored by another variable.

Usage

boxPlot(
  probesetId = NULL,
  geneSymbol = NULL,
  object,
  groups,
  main = NULL,
  colvec = NULL,
  colgroups = NULL,
  probe2gene = TRUE,
  addLegend = TRUE,
  legendPos = "topleft",
  ...
)

Arguments

probesetId	The probeset ID. These should be stored in the featureNames of the expressionSet object.
geneSymbol	The gene symbol. These should be stored in the column `Gene Symbol` in the featureData of the expressionSet object.
object	ExpressionSet object for the experiment
groups	String containing the name of the grouping variable. This should be a the name of a column in the pData of the expressionSet object.
main	Main title on top of the graph
colvec	Vector of colors to be used for the groups. If not specified, the default colors of a4palette are used.
colgroups	String containing the name of the variable to color the superimposed dots. This should be a the name of a column in the pData of the expressionSet object
probe2gene	Boolean indicating whether the probeset should be translated to a gene symbol (used for the default title of the plot)
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
...	Possibility to add extra plot options. See par

Value

A plot is drawn to the current device and probesetId are returned invisibly.

Author(s)

Willem Talloen

See Also

plot1gene

Examples

# simulated data set
esSim <- simulateData()
boxPlot(probesetId = 'Gene.1', object = esSim, groups = 'type', addLegend = FALSE)
# ALL data set
if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
  boxPlot(geneSymbol = 'HLA-DPB1', object = ALL, boxwex = 0.3,
		  groups = 'BTtype', colgroups = 'BT', legendPos='topright')
}

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