A function to plot by group means against each other.

Description

For a two sample comparison, as determined by group, and a specified KEGG pathway or GO category, per group means are computed and plotted against each other.

Usage

GOmnplot(x, eset, data = "hgu133plus2", group, ...)
KEGGmnplot(x, eset, data = "hgu133plus2", group, ...)

Arguments

Details

All probes in eset that map to the given category are determined. Then per group, per probe means are computed and plotted against each other. Extra parameters can be passed to the plot function via the dots argument.

Value

The matrix of per group means, for each probe.

Author(s)

R. Gentleman

See Also

KEGG2heatmap

Examples

  library("hgu95av2.db")
  data(sample.ExpressionSet)
  KEGGmnplot("04810", sample.ExpressionSet, sample.ExpressionSet$sex, 
             data = "hgu95av2")

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.
You are welcome to redistribute it under certain conditions.
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(annotate)
Loading required package: AnnotationDbi
Loading required package: stats4
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

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")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/annotate/GOmnplot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: GOmnplot
> ### Title: A function to plot by group means against each other.
> ### Aliases: GOmnplot KEGGmnplot KEGGmnplot,character,eSet,character-method
> ###   KEGGmnplot,character,matrix,character-method
> ### Keywords: manip
> 
> ### ** Examples
> 
>   library("hgu95av2.db")
Loading required package: org.Hs.eg.db


>   data(sample.ExpressionSet)
>   KEGGmnplot("04810", sample.ExpressionSet, sample.ExpressionSet$sex, 
+              data = "hgu95av2")
       31557_at 31699_at 31719_at 31720_s_at AFFX-HSAC07/X00351_3_at
Female 5769.618 238.9623 1659.094   1655.935                4760.580
Male   5851.949 245.2747 1456.260   1488.698                4949.658
       AFFX-HSAC07/X00351_3_st AFFX-HSAC07/X00351_5_at AFFX-HSAC07/X00351_5_st
Female                123.4877                3566.973                177.1625
Male                  110.3674                3472.315                183.6415
       AFFX-HSAC07/X00351_M_at AFFX-HSAC07/X00351_M_st
Female                4355.943                196.4948
Male                  4257.735                198.4687
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>