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.
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
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')
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(a4Base)
Loading required package: grid
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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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resource was removed from the the public domain before the most
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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/boxPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: boxPlot
> ### Title: Create a boxplot for a given gene.
> ### Aliases: boxPlot
>
> ### ** 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')
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Warning message:
In boxPlot(geneSymbol = "HLA-DPB1", object = ALL, boxwex = 0.3, :
Gene HLA-DPB1 corresponds to 2 probesets; only the first probeset ( 38095_i_at ) has been displayed on the plot.
>
>
>
>
>
> dev.off()
null device
1
>