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

Author(s)

W. Talloen

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")
}

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'contributors()' for more information and
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Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(a4Base)
Loading required package: grid
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Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

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    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

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  deprecated and future versions of Bioconductor may not have it
  available.  Users who want more current data are encouraged to look
  at the KEGGREST or reactome.db packages

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a4Base version 1.20.0

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/profilesPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: profilesPlot
> ### Title: Plot expression profiles of multiple genes or probesets
> ### Aliases: profilesPlot
> 
> ### ** 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")
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db


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