GeneAnswers (version 2.14.0)

getConnectedGraph: build and display a network for given IDs

Description

A function to build and display a network by different show types for given IDs and interaction Matrix with specified filtered IDs.

Usage

getConnectedGraph(graphIDs, idType=c('GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction', 'Customized'), edgeM=NULL, limitedLayers=FALSE, layers=6, treeMergeFilter=FALSE,
						searchAll=FALSE, showAllNodes=FALSE, directed=FALSE, direction=c('up', 'down', 'both'), filterGraphIDs=NULL, filterLayer=1, verbose=TRUE, ...)

Arguments

graphIDs

a character vector for given IDs

idType

type of IDs, could be one of 'GO', 'GO.BP', 'GO.CC', 'GO.MF', 'GeneInteraction' and 'Customized'

edgeM

a 2-column Matrix representing a network

limitedLayers

logic, user specified layers to stop search

layers

an integer, specify how many layers will be retrieved.

treeMergeFilter

logic, determine whether apply filterGraphIDs during searching a merged tree, see details

searchAll

logic, determine whether search all nodes

showAllNodes

logic, determine whether show all nodes based on searching result

directed

logic, the network is a directed or not

direction

search direction, it could be 'up', 'down' and 'both'. Valid for directed network only.

filterGraphIDs

a chacater vector for filtered IDs or a 2- or 3-column matrix for extra values.

filterLayer

an integer, specify where filterGraphIDs are applied.

verbose

logic, specify to show information or not.

...

other parameters used by 'buildNet'

Value

invisibly return a list containing elements to represent a network.

Details

Currently, if idType is 'GO', 'GO.BP', 'GO.CC' or 'GO.MF', edgeM will be ignore.

edgeM is a 2-column matrix. For directional connection, the direction is from column 1 elements to column 2 elements. For non-directional connection, each connection should be reversely presented twice, one is from column 1 element to column 2 element, while another is from column 2 element to column 1 element. In other words, non-directional connection is considered as two reverse directional connections.

filterGraphIDs are applied only at the filterLayer and more outer layers. This means the nodes between the filterLayer layer and the most external layer belong to the filterGraphIDs. The nodes between given graphIDs and the (filterLayer-1) layer are or are not from filterGraphIDs, but those nodes not in filterGraphIDs should be able to be finally connected by given graphIDs and filterGraphIDs.

The function at first searches a merged tree based on given IDs. During searching, filterGraphIDs could be applied if 'treeMergeFilter' is set to TRUE. If a merged tree is found, searching process stops unless 'searchAll' is set to TRUE. However, 'limitedLayers' is set to TRUE, searching process also stops when searching layers reach 'layers'. Only all filterGraphIDs specified nodes as well as given nodes will be displayed if 'showAllNodes' is set to FALSE, or all connected nodes will be displayed.

See buildnet for network layout.

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

buildNet

Examples

require(GeneAnswers)
example(GeneAnswers)
filterM <- cbind(rownames(getEnrichmentInfo(x)), -log2(getEnrichmentInfo(x)[,7]), getEnrichmentInfo(x)[,1])
## Not run: getConnectedGraph(rownames(getEnrichmentInfo(x))[c(1:5)],  filterGraphIDs=filterM,  output='fixed', directed=TRUE, direction='up', showAllNodes=T, searchAll=T)