plotCluster: Plotting the gene specific profiles for one given cluster of genes

Description

The function is plotting the profiles of the genes that belongs to the same cluster. It is not providing the clustering itself, just plotting the results of clustering from input. Optionally, the function can center the profiles around the gene-specific means.

Usage

plotCluster(DRdata, doseData, ORCMEoutput, clusterID, 
zeroMean=FALSE, xlabel, ylabel, main="")

Arguments

DRdata

the microarray data with rows corresponding to genes and columns corresponding to time points or different doses

doseData

indicates the dose levels

ORCMEoutput

the matrix of classification into clusters: each row represents one gene and columns found clusters. The matrix consist of the Booleans values, in each row there is only one of them TRUE which means that the gene was classified into the respective gene

clusterID

id of the cluster to be plotted

zeroMean

if TRUE, it centers the gene profiles around the gene-specific means, default is FALSE

xlabel

a title for the x axis

ylabel

a title for the y axis

main

an overall title for the plot

Value

Plot of the gene specific profiles dependent one the dose level (or time point) that are classified into the given cluster.

References

Lin D., Shkedy Z., Yekutieli D., Amaratunga D., and Bijnens, L. (editors). (2012) Modeling Dose-response Microarray Data in Early Drug Development Experiments Using R. Springer.

Cheng, Y. and Church, G. M. (2000). Biclustering of expression data. In: Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 1, 93-103.

Examples

Run this code

  data(doseData)
  data(geneData)

  
  dirData <- monotoneDirection(geneData = geneData,doseData = doseData)
  incData <- as.data.frame(dirData$incData)
  ORCMEoutput <- ORCME(DRdata=incData,lambda=0.15,phi=2)
  
  plotCluster(DRdata=incData,doseData=doseData, ORCMEoutput=ORCMEoutput,
  clusterID=4,zeroMean=FALSE, xlabel="Dose",ylabel="Gene Expression")