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Last data update: 2014.03.03

R: Plot coloured bound probes

plotBoundProbes

R Documentation

Plot coloured bound probes

Description

Scatterplot of bound probes in colour based on the method.

Usage

plotBoundProbes(xSet, sgrset, method=c("pairwise" , "compensation" , "increasedBinding"), 
                 bound.cutoff, diff.cutoff, cols=NULL, pcex=2)

Arguments

`xSet`	object of class ExpressionSet
`sgrset`	integer; specifying which data set to use from the ExpressionSet
`method`	a character string equal to “pairwise” , “increasedBinding” , “compensation”
`bound.cutoff`	numeric; threshold above probes are considered “bound”
`diff.cutoff`	numeric; difference threshold to determine if object 1 and object 2 are uniquely bound
`cols`	vector of colours to highlight probes, otherwise colours are set by default
`pcex`	a numerical vector giving the amount by which probe symbols should be scaled relative to the default

Details

Scatterplot of the bound probes in colour based on the selected method

Value

Coloured scatter plot

Author(s)

Bettina Fischer

Examples

  dataPath <- system.file("data",package="SimBindProfiles")
  load(file.path(dataPath,"SGR.RData"))
  plotBoundProbes(SGR, sgrset=c(1,2), method="pairwise", bound.cutoff=1.86, diff.cutoff=1.4)

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(SimBindProfiles)
Loading required package: Ringo
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: RColorBrewer
Loading required package: limma

Attaching package: 'limma'

The following object is masked from 'package:BiocGenerics':

    plotMA

Loading required package: Matrix
Loading required package: grid
Loading required package: lattice
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/SimBindProfiles/plotBoundProbes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotBoundProbes
> ### Title: Plot coloured bound probes
> ### Aliases: plotBoundProbes
> 
> ### ** Examples
> 
>   dataPath <- system.file("data",package="SimBindProfiles")
>   load(file.path(dataPath,"SGR.RData"))
>   plotBoundProbes(SGR, sgrset=c(1,2), method="pairwise", bound.cutoff=1.86, diff.cutoff=1.4)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>