geneAnswersConceptRelation {GeneAnswers} | R Documentation

## Display a network related to given concepts for a GeneAnswers instance

### Description

A function to display a network related to given concepts of a GeneAnswer instance

### Usage

    geneAnswersConceptRelation(x, showCats=c(1:5), conceptsIDs=NULL, directed=TRUE, direction=c('down', 'up', 'both'), catTerm=TRUE, catID=FALSE, nameLength='all', ...)

### Arguments

`x` | a GeneAnswers instance
`showCats` | a numeric or string vector specified categories
`conceptsIDs` | a vector or a data frame or matrix containing possible relative concepts, see details
`directed` | logic, the network is a directed or not
`direction` | search direction, it could be 'up', 'down' and 'both'. Valid for directed network only.
`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
`nameLength` | show how many first letters for long term names, 'all' for full name
`...` | other parameters used by 'getConnectedGraph'

### Details

conceptsIDs could be a character vector or a data frame or a matrix. As a character vector, it is a group of concept IDs or names depending on the given GeneAnswers instance, which are used to be a group of filters to draw a network relative to given concepts specified by showCats. When it is a data frame or matrix, it could be a 2- or 3-column data frame or matrix. The column 2 is always used to be represent nodes color, while the 3rd column is for size of nodes if available.

### Value

return a invisible list representing the network.

### 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

`getConnectedGraph`

### Examples

    require(GeneAnswers)
    example(GeneAnswers)
    ## Not run: geneAnswersConceptRelation(x, UP=FALSE, directed=TRUE, netMode='connection')

[Package GeneAnswers version 2.28.0 Index]