plot1gene: Create a Profile Plot for a given Gene

Description

Create a profile plot for a given gene. A profile plot displays the expression values (y-axis) by samples (x-axis), sorted by group. This is a useful working graph as samples can be directly identified. For presentation purposes, a boxPlot can also be considered. with jittered for readability of the plot.

Usage

plot1gene(probesetId = NULL, geneSymbol = NULL, object, groups, main = NULL, colvec = NULL,
	colgroups = NULL, probe2gene = TRUE, sampleIDs = TRUE, 
	addLegend = TRUE, legendPos = "topleft", cex = 1.5, ...)

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 name of a column in the pData of the expressionSet object.

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.

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.

probe2gene

Boolean indicating whether the probeset should be translated to a gene symbol (used for the default title of the plot)

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

cex

character expansion used for the plot symbols; defaults to 1.5

...

Further arguments, e.g. to add extra plot options. See par

Value

If a geneSymbol is given that has more than one probeSet, the plots for only the first probeSet is displayed. A character vector of corresponding probeset IDs is returned invisibly, so that one can check the profiles of the other related probeset IDs with an extra plot1gene statement If a probesetId is given, one single profile plot for the probeset is displayed.

References

~put references to the literature/web site here ~

Examples

Run this code

if (require(ALL)){
  data(ALL, package = "ALL")
  ALL <- addGeneInfo(ALL)

  # one variable (specified by groups)
  aa <- plot1gene(geneSymbol = 'HLA-DPB1', object = ALL, groups = "BT",
	    addLegend = TRUE, legendPos = 'topright')
  aa
  
  # two variables (specified by groups and colGroups)
  ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
  plot1gene(probeset = '1636_g_at', object = ALL, groups = 'BT',
      colgroups = 'mol.biol', legendPos='topright', sampleIDs = 'BT')    
}