tempNet: Creating a temporal network from graphs

In wanyuac/GeneMates: Analysing association and physical linkage between bacterial genes

Creating a temporal network from graphs

Description

This function creates a temporal network for visualisation from a list of Graph objects. Graphs in this list are named by years. Every member graph must consist of the same vertices and edges. In particular, when the network is undirectional, node order of each edge must be the same in the data frame defining edges.

Dependency: package network and networkDynamic. The package ndtv is required to display the output dynamic network as an animation.

Usage

tempNet(
  gs,
  v.label = "allele",
  e.tail = "node1",
  e.head = "node2",
  directed = FALSE,
  t.gap = 1,
  v.value = "count",
  v.value.base = 0,
  v.size.min = 1,
  v.size.max = 25,
  v.colour = "red",
  e.weight = "n_xy",
  e.weight.base = 1,
  e.weight.cutoff = 0,
  e.width.min = 1,
  e.width.max = 10,
  e.colour = "m",
  e.colour.low = "#FFA0A0",
  e.colour.high = "#FF0000",
  e.colour.num = 9
)

Arguments

gs	A GraphSet object with years as graph IDs.
v.label	A single name or index for the column from which vertex labels are drawn.
e.tail	Column name for tail vertices.
e.head	Column name for head vertices.
directed	A logical parameter specifying whether the network is directed or not. Default: FALSE (undirected).
t.gap	An integer or numeric argument determining the non-inclusive minimum difference (namely, t > t.gap rather than t >= t.gap) between two consecutive time points to be considered as not continuous. This arguments determines each onset and terminus range for edges.
v.value	A character or integer specifying the column in V(gs) used as the variable defining vertex sizes.
v.value.base	A numeric specifying the minimum value for the variable (column) defining vertex sizes. For instance, you may set v.size.base for a dynamic co-occurrence count where the expected minimum count is zero.
v.size.min	An integer for the minimum vertex size (when v.size.base is reached).
v.size.max	An integer for the maximum vertex size.
v.colour	A character vector of colours named by vertex labels.
e.weight	Column name or index in E(gs[[t]]) for edge widths.
e.weight.base	The minimum valid value of edge weights. It works in the same way as v.value.base.
e.weight.cutoff	Non-inclusive minimum edge weight that determines whether an edge is present at a time point.
e.width.min	Minimum edge width.
e.width.max	Maximum edge width.
e.colour	A column name or index for the attributed used for colour assignment.
e.colour.low	A character specifying the colour for edges of the least weight.
e.colour.high	A character specifying the colour for edges of the highest weight.
e.colour.num	An integer specifying the number of colours to be assigned.

Author(s)

Yu Wan ([e-mail])

wanyuac/GeneMates documentation built on Aug. 12, 2022, 7:37 a.m.