Scatter plots for pair of genes

Description

This function displays scatter plots for pair of genes that presented altered correlation values in Relevance Network analysis.

Usage

plotGenePair(obj, gene1, gene2, posL=NULL, rCor=TRUE)

Arguments

Details

This function only picks the result of the relNetworkM and display scatter plots for a pair of genes giving the regression lines and the correlation values for the two biological groups tested.

Value

This function don't return any object.

Author(s)

Gustavo H. Esteves <gesteves@vision.ime.usp.br>

See Also

maigesRelNetM, robustCorr, relNetworkM.

Examples

## Loading the dataset
data(gastro)

## Constructing the relevance network for sample
## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
  samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
  type="Rpearson")

## As the sample size is small, because we used a small fraction of the
## genes from the original dataset, this isn't so reliable.
plotGenePair(gastro.net, "KLK13", "EVPL")

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(maigesPack)
Loading required package: convert
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: limma

Attaching package: 'limma'

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

    plotMA

Loading required package: marray
Loading required package: graph
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/maigesPack/plotGenePair.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plotGenePair
> ### Title: Scatter plots for pair of genes
> ### Aliases: plotGenePair
> ### Keywords: classes
> 
> ### ** Examples
> 
> ## Loading the dataset
> data(gastro)
> 
> ## Constructing the relevance network for sample
> ## 'Tissue' comparing 'Neso' and 'Aeso' for the 1st gene group
> gastro.net = relNetworkM(gastro.summ, sLabelID="Tissue", 
+   samples = list(Neso="Neso", Aeso="Aeso"), geneGrp=11,
+   type="Rpearson")
> 
> ## As the sample size is small, because we used a small fraction of the
> ## genes from the original dataset, this isn't so reliable.
> plotGenePair(gastro.net, "KLK13", "EVPL")
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>