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.
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.
Author(s)
S. Osselaer, W. Talloen, T. Verbeke
References
~put references to the literature/web site here ~
See Also
plotCombination2genes, boxPlot
Examples
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')
}
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> 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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Attaching package: 'S4Vectors'
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colMeans, colSums, expand.grid, rowMeans, rowSums
Loading required package: annaffy
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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
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Attaching package: 'MASS'
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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
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Loading required package: multtest
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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/plot1gene.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot1gene
> ### Title: Create a Profile Plot for a given Gene
> ### Aliases: plot1gene
> ### Keywords: dplot
>
> ### ** Examples
>
> 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')
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
Warning message:
In plot1gene(geneSymbol = "HLA-DPB1", object = ALL, groups = "BT", :
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
>