Hi,

In R-controlled Cytoscape, I would like to select nodes within regions with more than two nodes OR more than one edge. With the code below, nodes 1, 4 and 5 get selected. My goal is to select only nodes 4 and 5 (see image).

Any help would be greatly appreciated. Thanks!

David

library(RCy3)
nodes <- data.frame(
  id = c("node 0","node 1","node 2","node 3", "node 4", "node 5"),
  stringsAsFactors = FALSE)

edges <- data.frame(
  source = c("node 0","node 0","node 0","node 2", "node 4"),
  target = c("node 1","node 2","node 3","node 3", "node 5"),
  stringsAsFactors = FALSE)

createNetworkFromDataFrames(nodes, edges, title = "test")

createDegreeFilter(
  filter.name = 'degree filter',
  criterion = c(2,3),
  predicate = 'IS_NOT_BETWEEN')

If I understand correctly, you want to select all binary pairs of connected nodes. Here's one approach, basically, select the nodes your DON'T want and then inverse selection:

library(RCy3)
nodes <- data.frame(
  id = c("node 0","node 1","node 2","node 3", "node 4", "node 5"),
  stringsAsFactors = FALSE)

edges <- data.frame(
  source = c("node 0","node 0","node 0","node 2", "node 4"),
  target = c("node 1","node 2","node 3","node 3", "node 5"),
  stringsAsFactors = FALSE)

createNetworkFromDataFrames(nodes, edges, title = "test")

createDegreeFilter(
  filter.name = 'degree filter',
  criterion = c(1,1),
  predicate = 'IS_NOT_BETWEEN')

selectFirstNeighbors()

invertNodeSelection()