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

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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

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

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