groupReport: Generate a multigroup Concepts-genes analysis report

Description

Function to generate a html format top multigroup Concepts-genes analysis report based on a given GeneAnswers instance list. Currently, this function only works at Mac platform and Java 1.6 or latest version is required.

Usage

groupReport(dataMatrix, gAList, topCat=10, methodOfCluster=c('mds', 'sort'), matrixOfHeatmap=NULL, clusterTable=c('geneNum', 'pvalue', NULL), catTerm=TRUE,
		fileName = "multiConceptsGenes.html", title='Multigroup Genes Concepts Analysis', catType=c('GO', 'KEGG', 'DOLITE', 'REACTOME.PATH', 'CABIO.PATH', 'Unknown'),
		reverseOfCluster=FALSE,  colorValueColumn = NULL, annLib=c('org.Hs.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db', 'org.Dm.eg.db'), nameLength=94, addID=TRUE, interactive=FALSE,
		bgColor='#ffffff', keepCytoscapeFiles=TRUE, wordleOn=FALSE, ...)

Arguments

dataMatrix

a top concepts-genes matrix generated by getConceptTable.

gAList

a GeneAnswers instance list.

topCat

number to specify how many top concepts-genes analysis will show.

methodOfCluster

cluster method

matrixOfHeatmap

NULL or a concepts-genes matrix generated by getConceptTable, which is used to show enrichment test significance for each concept.

clusterTable

cluster data to specify which type of values will be used for cluster.

catTerm

logic, determine whether mapping category IDs to names

fileName

output html file name

title

output html title

catType

category type, current version supports 'GO', 'KEGG', 'DOLITE', 'REACTOME.PATH', 'CABIO.PATH' and customized annotation libraries, 'Unknown'.

reverseOfCluster

logic, whether reverse the cluster order.

colorValueColumn

numbers or column names of geneInput slots of the given GeneAnswers instance list to specify the colors of leaves

annLib

annotation librarry names, current version supports 'org.Hs.eg.db', 'org.Rn.eg.db', 'org.Mm.eg.db' and 'org.Dm.eg.db'.

nameLength

show how many first letters for long term names, 'all' for full name, default value is 94.

addID

logic, add term IDs following term names or not

interactive

logic, determine whether network is interactive or not. Interactive network requires java and flash supports.

bgColor

a R compatible color for html background color.

keepCytoscapeFiles

logic, determine whether to keep cytoscape files if interactive is set to TRUE

wordleOn

logic, determine whether a geneRif based worl cloud is generated or not. This requires an internet connection.

...

other parameters used by 'sort'

Value

no value returned

Details

In general, a html format top multigroup Concepts-genes analysis report is generated. It includes a multigroup concepts-genes table, several concepts-genes networks figures and a couple of tables containing genes and their information. colorValueColumn could be NULL, column name or a same length column-name vector as length of the given GeneAnswers instantce list. No color for genes if it is NULL. All of GeneAnswers instances are applied color for genes based on the same column name if the length is one. Or the colors of genes in concepts-genes networks are based on the same length column-name vector. If catType is not set to 'Unknown', catTerm in function getConceptTable should be set to FALSE.

References

Feng, G., Du, P., Krett, N., Tessel, M., Rosen, S., Kibbe, W.A. and Lin, S.M., 'A collection of bioconductor methods to visualize gene-list annotations', BMC Research Notes 2010, 3:10

Examples

Run this code

data(sampleGroupsData)
gAKEGGL <- lapply(sampleGroupsData, geneAnswersBuilder, 'org.Hs.eg.db', categoryType='KEGG', pvalueT=0.1, verbose=FALSE)
output<- getConceptTable(gAKEGGL, catTerm=FALSE, items='geneNum')
## Not run: groupReport(output[[1]], gAKEGGL,  matrixOfHeatmap=output[[2]], clusterTable=NULL, fileName='KEGGtest.html',  catType='KEGG', colorValueColumn=colnames(sampleGroupsData[[1]])[-1])

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