geneAnswersConceptNet {GeneAnswers} | R Documentation

## Concept-Gene Networking Plotting

### Description

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

### Usage

    geneAnswersConceptNet(x, colorValueColumn = NULL, centroidSize = c("pvalue", "geneNum", "foldChange", "oddsRatio", "correctedPvalue"), output = c("fixed", "interactive", "none"), showCats=c(1:5), geneLayer=1, edgeM=NULL, catTerm=FALSE, geneSymbol=FALSE, catID=FALSE, nameLength='all', ...)

### Arguments

`x` | a GeneAnswers instance.
`colorValueColumn` | number or column name of geneInput slot to specify the colors of leaves
`centroidSize` | type to represent the size of concepts.
`output` | output type of final output.
`showCats` | a numeric or string vector specified categories
`geneLayer` | an integer, specify how many layers of genes connecting to concepts
`edgeM` | a 2-column Matrix representing a network
`catTerm` | a logic value to specify whether mapping category IDs to category names
`geneSymbol` | a logic value to specify whether mapping gene IDs to gene symbols
`catID` | a logic value to specify whether show category IDs when catTerm is set to TRUE
`nameLength` | show how many first letters for long term names, 'all' for full name
`...` | other parameters used by 'geneConceptNet'

### Details

colorValueColumn specifies which column of the geneInput of the GeneAnswers instance is used for color of nodes. 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. None will not output any figure but a list. See details in `geneConceptNet`

### Value

One concept-gene 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

`getMultiLayerGraphIDs`, `geneConceptNet`

### Examples

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

[Package GeneAnswers version 2.28.0 Index]