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Last data update: 2014.03.03

R: Function to plot the gene expression profiles

traceGeneProfiles

R Documentation

Function to plot the gene expression profiles

Description

This function is used for plotting the target and parent gene expression profiles.

Usage

traceGeneProfiles(targetData, parentData,  dataDescription=NULL,
targetColor = "grey", parentColor = "blue", onepage=TRUE)

Arguments

`targetData`	A matrix (or a vector if only one target gene) with the temporal gene expression measurements for the target genes (i.e. the genes whose regulation factors are looked for). Target genes are shown in row and expression values in column.
`parentData`	A matrix (or a vector if only 1 parent gene) with the temporal gene expression measurements for the proposed parent genes (i.e. potential regulation factors). Parent genes are shown in row and expression values in column.
`dataDescription`	(Required only when the gene expression measurements contain repeated values for the same time points). A vector indicating the ordering of the time measurements in the data. For example dataDescription=rep(1:n, each=2), if there are two measurements for each time point AND the repetitions for each time point are next to each other. Note that temporal gene expression measurements have to be organized identically in arguments `targetData` and `parentData` (optional, default: `dataDescription=NULL`).
`targetColor`	Color for plotting the target genes expression profiles (optional, default `targetColor= "grey"`)
`parentColor`	Color for plotting the parent genes expression profiles (optional, default `parentColor= "blue"`)
`onepage`	Boolean, if `TRUE`, all output pictures are plotted on one page only (optional, default: `onepage=TRUE`.

Value

NULL

Author(s)

S. Lebre and G. Lelandais.

References

Statistical inference of the time-varying structure of gene-regulation networks S. Lebre, J. Becq, F. Devaux, M. P. H. Stumpf, G. Lelandais, BMC Systems Biology, 4:130, 2010.

Examples

# Load the R package ARTIVA
library(ARTIVA)

# Load the dataset with simulated gene expression profiles
data(simulatedProfiles)

# Name of the target gene to be analyzed with ARTIVA 
targetGene = 1

# Names of the parent genes (typically transcription factors) 
parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")

# Plot of the gene expression profiles for target gene and parent genes
traceGeneProfiles(targetData= simulatedProfiles[targetGene,], 
		  parentData= simulatedProfiles[parentGenes,])

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)

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> library(ARTIVA)
Loading required package: MASS
Loading required package: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

Loading required package: gplots

Attaching package: 'gplots'

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

    lowess

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/ARTIVA/traceGeneProfiles.Rd_%03d_medium.png", width=480, height=480)
> ### Name: traceGeneProfiles
> ### Title: Function to plot the gene expression profiles
> ### Aliases: traceGeneProfiles
> ### Keywords: graphics util
> 
> ### ** Examples
> 
> # Load the R package ARTIVA
> library(ARTIVA)
> 
> # Load the dataset with simulated gene expression profiles
> data(simulatedProfiles)
> 
> # Name of the target gene to be analyzed with ARTIVA 
> targetGene = 1
> 
> # Names of the parent genes (typically transcription factors) 
> parentGenes = c("TF1", "TF2", "TF3", "TF4", "TF5")
> 
> # Plot of the gene expression profiles for target gene and parent genes
> traceGeneProfiles(targetData= simulatedProfiles[targetGene,], 
+ 		  parentData= simulatedProfiles[parentGenes,])
> 
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>