visualize.community: visualize ego gene X, its k step neighbours, and the W gene...

In LANDD: Liquid Association for Network Dynamics Detection

Description

visualize ego gene X, its k step neighbours, and the W gene communities: Generate a graph with different community in different colors. visualize.community()is used to create a graph to display the layout of genes X, X's k-step neighborhood, W and their corresponding community.

Usage

visualize.community(graph, kernel.result, x, k = 2, cutoff = 1,
  community.min = 5, path = NULL)

Arguments

graph	The igraph object of gene network.
kernel.result	The result of graph.kd which finds genes W of a gene X.
x	The gene the plot is generated for.
k	The degree of the neighborhood of X.
cutoff	A threshold to filter gene W.
community.min	The minimum size of the community of W.
path	The path where the result graph is saved to. The default path is the original path of input graph.

Value

a graph displays genes X, X's k-step neighborhood, and W gene communities in different colors.

Examples

## Not run: 
kernel <- graph.kd(relate.matrix,g,smoothing.normalize = "one")
visualize(g,kernel,x,k=2,cutoff=1,community.min=5,path=NULL)
## End(Not run)

LANDD documentation built on May 1, 2019, 8:12 p.m.