Description Usage Arguments Value Author(s) Examples

View source: R/visualizeBiopax.R

This function gracefully removes nodes from a regulatory graph. If the node to be removed has both parent and child nodes, these are connected directly. The weight of the new direct edge is the product of multiplying the incomming and outgoing edge weights of the original node.

1 | ```
removeNodes(graph, nodes)
``` |

`graph` |
graphNEL |

`nodes` |
vector of node names specifiying which nodes to remove. |

Returns a graph with specified nodes removed.

Frank Kramer

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
# load data and retrieve wnt pathway
data(biopaxexample)
pwid1 = "pid_p_100002_wntpathway"
mygraph1 = pathway2RegulatoryGraph(biopax, pwid1)
mygraph1 = layoutRegulatoryGraph(mygraph1)
# retrieve all nodes
nodes = nodes(mygraph1)
# random expression data for your nodes
values = rnorm(length(nodes), mean=6, sd=2)
# color nodes of the graph
mygraph1 = colorGraphNodes(mygraph1, nodes, values, colors="greenred")
# plot the now colored graph
plotRegulatoryGraph(mygraph1, layoutGraph=FALSE)
``` |

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