clipper (version 1.12.0)

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

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", layout="jgraph-spring")

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'

layout

a 'string' of choice among the values returned by 'getLayoutNames', default = 'jgraph-spring'

Details

Requires the RCytoscape package.

See Also

clipper

Examples

## Not run: if (require(graphite)) {
#   if (requireNamespace("RCytoscape")){
#     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",
# "1029;4193;7157","1019;1021;1026;1029;595")
# plotInCytoscape(graph,path)
#     }
#   ## End(Not run)