netview: NetView R

In esteinig/netview: Mutual k-Nearest-Neighbour Networks for Population Analysis

Description

Generate mutual nearest-neighbour graphs for population analysis and visualization with iGraph and networkD3.

Usage

netview(distMatrix, metaData, k=1:60, cluster=TRUE, ...)

Arguments

distMatrix	Symmetrical distance matrix for NetView (N x N)
metaData	Data frame with meta data for each sample (N), ordered as samples in distMatrix; required columns 'ID', 'Group' and 'Colour'
tree	Rooted phylogeny for construction of a cophenetic distance matrix [ phylo, NULL ]
k	Range of parameter k for mutual k-nearest-neighbour search [ vector of integers, 10:60 ]
cluster	Decorate graph objects with the results of community detection analyses, configure via netviewOptions [ bool, FALSE ]
mst	Include edges of the minimum spanning tree associated with the data [ bool, FALSE ]
networkD3	Return networks visualizations with networkD3, configure via netviewOptions [ bool, FALSE ]
save	Save graphs as GML or visualizations with networkD3 as HTML [ bool, FALSE ]
project	Project directory for saving graphs and networkD3 [ str, 'netview' ]
options	Options from netviewOptions() [ list, netviewOptions() ]

Details

For examples and tutorials, please see our GitHub Repository: https://github.com/esteinig/netview

Value

List of graph objects or widgets from networkD3.

esteinig/netview documentation built on Feb. 8, 2022, 7:17 a.m.