Diggit plot

Description

This function generate plots for the diggit conditional analysis

Usage

## S4 method for signature 'diggit'
plot(x, mr = NULL, cluster = NULL, sub = NULL, ...)

Arguments

Value

Nothing, plots are generated in the default output device

Examples

data(gbm.expression, package="diggitdata")
data(gbm.cnv, package="diggitdata")
data(gbm.aracne, package="diggitdata")
dobj <- diggitClass(expset=gbmExprs, cnv=gbmCNV, regulon=gbmTFregulon)
dobj <- fCNV(dobj)
dobj <- aqtl(dobj, mr=c("CEBPD", "STAT3"), fcnv.adjust="fdr", verbose=FALSE)
dobj <- conditional(dobj, pheno="subtype", group1="MES", group2="PN", mr="STAT3", verbose=FALSE)
plot(dobj, cluster="3")

Results

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(diggit)
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")'.

> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/diggit/diggit-plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot,diggit-method
> ### Title: Diggit plot
> ### Aliases: plot plot,diggit-method
> 
> ### ** Examples
> 
> data(gbm.expression, package="diggitdata")
> data(gbm.cnv, package="diggitdata")
> data(gbm.aracne, package="diggitdata")
> dobj <- diggitClass(expset=gbmExprs, cnv=gbmCNV, regulon=gbmTFregulon)
> dobj <- fCNV(dobj)
> dobj <- aqtl(dobj, mr=c("CEBPD", "STAT3"), fcnv.adjust="fdr", verbose=FALSE)
> dobj <- conditional(dobj, pheno="subtype", group1="MES", group2="PN", mr="STAT3", verbose=FALSE)
> plot(dobj, cluster="3")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>