geneAnswersConcepts {GeneAnswers} | R Documentation

## Concept-Gene Networking Plotting

### Description

A function to generate a concept-gene network by given gene information

### Usage

    geneAnswersConcepts(x, centroidSize=c('geneNum', 'pvalue', 'foldChange', 'oddsRatio', 'correctedPvalue'), output=c('fixed','interactive'), showCats=c(1:5), catTerm=FALSE, catID=FALSE)

### Arguments

`x` | a GeneAnswers instance.
`centroidSize` | type to represent the size of concepts.
`output` | output type of final output.
`showCats` | a numeric or string vector specified categories
`catTerm` | a logic value to specify whether mapping category IDs to category names
`catID` | a logic value to specify whether show category IDs when catTerm is set to TRUE

### Details

centroidSize could be one of "geneNum", "pvalue", "foldChange", "oddsRatio", "correctedPvalue". Each one defines to which the size of cencept dot is proportional geneNum: number of genes connecting to the concept pvalue: p value of enrichment test foldChange: fold of gene overrepresent in concepts oddsRatio: odds ratio of enrichment test correctedPvalue: adjusted p value of enrichment test output defines whether the final figure is interactive or not. Interactive figure calls igraph package to generate a tck/tk canvas. Fixed figure is a non-interactive png figure.

### Value

One category-linkage figure is generated. It could be a R figure or tcltk figure depends on how the user set parameter output.

### 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

`categoryNet`

### Examples

    example(GeneAnswers)
    ## Not run: geneAnswersConcepts(x, centroidSize='pvalue', output='interactive')

[Package GeneAnswers version 2.24.0 Index]