Radar is a function that plots the top enriched GO terms for the first and second level of analysis in a radar plot. The number of terms to be displayed can be set.
a character string specifying if the plot is saved in jpeg (jpeg), postscript (postscript), pdf (pdf) format, or it is simply displayed on the screen(on screen). By default this value is on screen.
n.nodes.1stlevel
a numeric value specifying the number of top enriched GO terms, from the first level, that will be represented on the plot. By default the value is set to 5.
n.nodes.2ndlevel
a numeric value specifying the number of top enriched GO terms, from the second level, that will be represented on the plot. By default the value is set to 5.
mult.cor
a boolean variable specifying whether the displayed significance values are multiple test corrected or the original p-values obtained from the selected enrichment method. By default it is set to TRUE.
...
if the class of object is GOsets, it accepts a character string named ontology selecting the GO ontology of interest, either CC,BP or MF.
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)
R is free software and comes with ABSOLUTELY NO WARRANTY.
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Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
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(tRanslatome)
Loading required package: limma
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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
Loading required package: Biobase
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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> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/tRanslatome/Radar.Rd_%03d_medium.png", width=480, height=480)
> ### Name: Radar
> ### Title: RadarEnrichedHelpfile
> ### Aliases: Radar
> ### Keywords: DEGs GO Regulatory enrichment analysis radar plot
>
> ### ** Examples
>
> data(tRanslatomeSampleData)
> Radar(CCEnrichment)
[1] "GO:0005759"
[1] "mitochondrial matrix"
[1] "GO:0042627"
[1] "chylomicron"
[1] "GO:0034361"
[1] "very-low-density lipoprotein particle"
[1] "GO:0034366"
[1] "spherical high-density lipoprotein parti..."
[,1] [,2] [,3] [,4]
[1,] 1.452533 3.340559 4.512720 1.638965
[2,] 1.427709 1.427709 2.390726 1.489857
>
>
>
>
>
> dev.off()
null device
1
>