ccOutCyt-methods: Methods for Function 'ccOutCyt' in Package 'categoryCompare'

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

Description

Passes a ccCompareResult object to Cytoscape for interactive visualization of ccCompare results.

Details

Note that only some basic, required methods have been imported from RCy3 for use with categoryCompare, and these are hidden in the functions within categoryCompare and are not visible to the user. If access to all the functionality of RCytoscape is desired (and trust me, there is a lot of useful stuff in there), then the user should use library(RCy3) directly.

It should also be noted that deletion of edges via RCy3 is slow, so some edge filtering should be done by breakEdges prior to using ccOutCyt.

Methods

signature(ccCompRes = "ccCompareResult", ccOpts = "ccOptions", ...)

At a minimum, this method requires a ccCompareResult and a ccOptions to work.

... may include:

layout = "character"

to override the default layout set by ccCompare, as well as options

postText = "character"

to add a user set string to the Cytoscape window

In addition, any of the arguments to CytoscapeWindow may also be set, such as host or port.

See Also

ccCompareResult ccOptions ccCompare CytoscapeWindowClass

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)
	Sys.sleep(10)
	RCy3::deleteWindow(cwObj)
	}

## End(Not run)

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