string containing the name of the grouping variable
addLegend
Logical value to indicate whether a legend needs to be drawn.
legendPos
Position on the graph where to put the legend
probe2gene
should the probeset be translated to a gene symbol
(used for the default title of the plot)
colvec
a character vector of colors. If not specified it will be
automatically generated by a4palette
...
This allows to specify typical arguments in the plot function
Value
If a gene id is given, the plots for only the first probeset is displayed
and a character vector of corresponding probeset IDs is returned invisibly.
It is a list containing
probeset1
Probeset ids measuring 'gene1'
probeset1
Probeset ids measuring 'gene1'
If a probeset id is given, one single profile plot for the probeset is
displayed.
Author(s)
W. Talloen, T. Verbeke
See Also
plot1gene
Examples
if (require(ALL)){
data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
aa <- plotCombination2genes(geneSymbol1 = 'HLA-DPB1', geneSymbol2 = 'CD3D',
object = ALL, groups = "BT",
addLegend = TRUE, legendPos = 'topright')
aa
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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Platform: x86_64-pc-linux-gnu (64-bit)
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Type 'demo()' for some demos, 'help()' for on-line help, or
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> library(a4Base)
Loading required package: grid
Loading required package: Biobase
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: 'BiocGenerics'
The following objects are masked from 'package:parallel':
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following objects are masked from 'package:stats':
IQR, mad, xtabs
The following objects are masked from 'package:base':
Filter, Find, Map, Position, Reduce, anyDuplicated, append,
as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
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")'.
Loading required package: AnnotationDbi
Loading required package: stats4
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Loading required package: S4Vectors
Attaching package: 'S4Vectors'
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colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: annaffy
Loading required package: GO.db
Loading required package: KEGG.db
KEGG.db contains mappings based on older data because the original
resource was removed from the the public domain before the most
recent update was produced. This package should now be considered
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
Loading required package: mpm
Loading required package: MASS
Attaching package: 'MASS'
The following object is masked from 'package:AnnotationDbi':
select
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
mpm version 1.0-22
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Attaching package: 'genefilter'
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Loading required package: limma
Attaching package: 'limma'
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Loading required package: multtest
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Attaching package: 'Matrix'
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Attaching package: 'a4Core'
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Loading required package: gplots
Attaching package: 'gplots'
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a4Base version 1.20.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/plotCombination2genes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotCombination2genes
> ### Title: Plot a Combination of Two Genes
> ### Aliases: plotCombination2genes
> ### Keywords: dplot
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+
+ aa <- plotCombination2genes(geneSymbol1 = 'HLA-DPB1', geneSymbol2 = 'CD3D',
+ object = ALL, groups = "BT",
+ addLegend = TRUE, legendPos = 'topright')
+ aa
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
$probeset1
[1] "38095_i_at" "38096_f_at"
$probeset2
[1] "38319_at"
Warning message:
In plotCombination2genes(geneSymbol1 = "HLA-DPB1", geneSymbol2 = "CD3D", :
Gene1 HLA-DPB1 corresponds to 2 probesets; only the first probeset ( 38095_i_at ) has been displayed on the plot.
>
>
>
>
>
> dev.off()
null device
1
>