Generic function to draw a volcano plot. A volcano plot is a graph that allows to
simultaneously assess the P values (statistical significance) and log ratios
(biological difference) of differential expression for the given genes.
Usage
volcanoPlot(x, y, pointLabels, ...)
Arguments
x
either an object of class 'tTest', of class 'limma' or a numeric vector of
log ratios, i.e. the log of the fold change values; the names of the logRatio vector
will be used to display the names of the most interesting genes
y
should not be given if an object of class 'tTest' or 'limma' is passed as
argument 'x'; if 'x' is a numeric vector of log ratios, 'y' should be given and
should be a numeric vector of P-values indicating the statistical significance
pointLabels
Labels for points on the volcano plot that are interesting
taking into account both the x and y dimensions; typically this is a
vector of gene symbols; most methods can access the gene symbols directly from
the object passed as 'x' argument; the argument allows for custom labels if
needed
...
further arguments to specific methods
Value
The volcano plot is drawn to the current device.
Author(s)
Tobias Verbeke, based on code by Willem Talloen
References
Goehlmann, H. and W. Talloen (2009). Gene Expression Studies Using Affymetrix
Microarrays, Chapman & Hall/CRC, pp. 148 - 153.
See Also
See volcanoplotter
Examples
if (require(ALL)){
data(ALL, package = "ALL")
ALL <- addGeneInfo(ALL)
ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
tTestRes <- tTest(object = ALL, groups = "BTtype", probe2gene = TRUE)
volcanoPlot(tTestRes)
}
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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'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(a4Base)
Loading required package: grid
Loading required package: Biobase
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Attaching package: 'BiocGenerics'
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clusterExport, clusterMap, parApply, parCapply, parLapply,
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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
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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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a4Base version 1.20.0
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/a4Base/volcanoPlot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: volcanoPlot
> ### Title: Draw a Volcano Plot
> ### Aliases: volcanoPlot
> ### Keywords: dplot
>
> ### ** Examples
>
> if (require(ALL)){
+ data(ALL, package = "ALL")
+ ALL <- addGeneInfo(ALL)
+ ALL$BTtype <- as.factor(substr(ALL$BT,0,1))
+
+ tTestRes <- tTest(object = ALL, groups = "BTtype", probe2gene = TRUE)
+ volcanoPlot(tTestRes)
+ }
Loading required package: ALL
Loading required package: hgu95av2.db
Loading required package: org.Hs.eg.db
>
>
>
>
>
> dev.off()
null device
1
>