plotInCytoscape: Plot a pathway graph in Cytoscape highlighting the relevant...

In clipper: Gene Set Analysis Exploiting Pathway Topology

Description

Renders the topology of a pathway as a Cytoscape graph and marks the genes of the selected path.

Usage

plotInCytoscape(graph, path, color="#6699FF", main="graph")

Arguments

graph	a graphNEL object.
path	vector summarizing a path (a rows of clipper output matrix).
color	color code string: genes of the most involved fragment will be colored using color. Deafult = "#6699FF"
main	a graph name to be used in Cytoscape. Default = 'graph'

Details

Requires the RCy3 package.

See Also

clipper

Examples

## Not run: if (require(graphite)) {
  if (requireNamespace("RCy3")){
    kegg  <- pathways("hsapiens", "kegg")
    graph <- pathwayGraph(convertIdentifiers(kegg$'Chronic myeloid leukemia', "entrez"))
}
    path <- c(3,17,5,9,13.04,2.60,0.209,0.321,"6,7,8,9,10","3,5,6,7,8,9,10,14,17","ENTREZID:1029;ENTREZID:4193;ENTREZID:7157","ENTREZID:1019;ENTREZID:1021;ENTREZID:1026;ENTREZID:1029;ENTREZID:595")
plotInCytoscape(graph,path)
    }
  
## End(Not run)

clipper documentation built on Nov. 8, 2020, 6:18 p.m.