cytOutNodes-methods: Methods for Function 'cytOutNodes'

In categoryCompare: Meta-analysis of high-throughput experiments using feature annotations

Description

Allows export of currently selected nodes in the Cytoscape window for data export

Methods

signature(descStr = "character", cwObj = "numeric", saveObj = "list")

descStr is a string describing the nodes that are currently selected, cwObj is the CytoscapeWindow that the nodes are in, and then saveObj is a previously generated cytOutNodes list, and is optional.

Examples

## Not run: 
hasCy <- (if (.Platform$OS.type %in% "windows") {
(length(grep("Cytoscape", system("tasklist", intern=TRUE))) > 0)})

if hasCy {
	ccResults$BP <- breakEdges(ccResults$BP, 0.8)
	cwObj <- ccOutCyt(ccResults$BP,ccOpts)
	# user selects some nodes in Cytoscape
	RCy3::selectNodes(cwObj, c("GO:0007017", "GO:0000226", "GO:0007051", "GO:0007052"))
	savedNodes <- cytOutNodes("random1", cwObj) # save them
	# and selects some other nodes
	RCy3::selectNodes(cwObj,
	c("GO:0071103", "GO:0034728", "GO:0006323", "GO:0030261", "GO:0006334"),
	preserve.current.selection=FALSE)
	savedNodes <- cytOutNodes("random2", cwObj, savedNodes)

	}

## End(Not run)

categoryCompare documentation built on Nov. 8, 2020, 5:59 p.m.