Plot nested design structure.

Description

plotDesign returns a plot with different color strips representing different factors relating to the study design. genes.

Usage

plotDesign(anno, Factors, anno.names = Factors, orderby = NULL)

Arguments

Value

plotDesign returns a plot.

Author(s)

Saskia Freytag

Examples

library(bladderbatch)
data(bladderdata)
expr.meta <- pData(bladderEset)
plotDesign(expr.meta, c("cancer", "outcome", "batch"),
c("Diagnosis", "Outcome", "Batch"), orderby="batch")

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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> library(RUVcorr)
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/RUVcorr/plotDesign.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotDesign
> ### Title: Plot nested design structure.
> ### Aliases: plotDesign
> 
> ### ** Examples
> 
> library(bladderbatch)
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")'.

> data(bladderdata)
> expr.meta <- pData(bladderEset)
> plotDesign(expr.meta, c("cancer", "outcome", "batch"),
+ c("Diagnosis", "Outcome", "Batch"), orderby="batch")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>