drawTable {GeneAnswers} | R Documentation

## 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'

### 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.

### Value

No return value.

### Author(s)

Gang Feng, Pan Du and Simon Lin

### 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)

[Package GeneAnswers version 2.22.0 Index]