LANDD (version 1.1.0)

visualize.community: 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.

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)