GeneAnswers (version 2.14.0)

drawTable: Concept-Gene Networking Plotting

Description

A function to generate a multigroup concepts-genes table

Usage

drawTable(dataMatrix, topCat=10, heatMap=TRUE, matrixOfHeatmap=NULL, clusterTable=c('geneNum', 'pvalue', NULL), methodOfCluster=c('mds', 'sort'), mar=c(1,5,5,8), 
			addRowLabel=TRUE, cex.axis=c(1.1, 0.9), reverseOfCluster=FALSE, xGridLine=FALSE, colorBar=TRUE, newWindow=TRUE, endOfColBar=c('> 0.01', 'Minimum of p values'), heatMapColor=c('#00ff00','#ffffff'), canvasWidth=NULL, canvasHeight=NULL, ...)

Arguments

dataMatrix

a top concepts-genes matrix generated by getConceptTable.

topCat

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

heatMap

logic, determine whether the multiple group concepts-genes table is presented by heatmap.

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.

methodOfCluster

cluster method

mar

marginal parameter for table, please see par

addRowLabel

logic, whether add row names

cex.axis

font size parameter for table, please see par

reverseOfCluster

logic, whether reverse the cluster order.

xGridLine

logic, whether add horizontal line in table or not

colorBar

logic, whether show color bar or not

newWindow

logic, whether present table in current active window or not

endOfColBar

a character string for color bar.

heatMapColor

a two R color element vector to define maximum and minimum colors.

canvasWidth

width of the canvas, the default is NULL, the value will be determined by the function.

canvasHeight

height of the canvas, the default is NULL, the value will be determined by the function.

...

other parameters used by 'sort'

Value

No return value.

Details

an image based multigroup concepts-genes table is generated. If heatmap is on, the statistical significant cells are shaded by different level green. Specified top gene amounts are highlighted as red.

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

See Also

See Also as getConceptTable, groupReport

Examples

data(sampleGroupsData)
gAKEGGL <- lapply(sampleGroupsData, geneAnswersBuilder, 'org.Hs.eg.db', categoryType='KEGG', pvalueT=0.1, verbose=FALSE)
#output<- getConceptTable(gAKEGGL, items='geneNum')
## Not run: drawTable(output[[1]], matrixOfHeatmap=output[[2]], mar=c(2,15,3,2), clusterTable=NULL)