diff_plot: plot difference network

In MarcOhlmann/metanetwork: Handling and Representing Trophic Networks in Space and Time

plot difference network

Description

Function to represent difference between two networks belonging to a metanetwork with specific layout ('TL-tsne' or group 'TL-tsne') using either 'ggnet' or 'visNetwork' visualisation. This function represent the difference between g1 and g2 (g1-g2).

Usage

diff_plot(
  metanetwork,
  g1,
  g2,
  beta = 0.1,
  mode = "TL-tsne",
  vis_tool = "ggnet",
  edge_thrs = NULL,
  edge_diff_thrs = NULL,
  layout_metaweb = FALSE,
  flip_coords = FALSE,
  alpha_per_group = NULL,
  alpha_per_node = NULL,
  TL_tsne.config = TL_tsne.default,
  nrep_ly = 1,
  ggnet.config = ggnet.default,
  visNetwork.config = visNetwork.default
)

Arguments

metanetwork	object of class 'metanetwork'
g1	network (of class 'igraph') of metanetwork
g2	network (of class 'igraph') of metanetwork
beta	the diffusion parameter of the diffusion kernel, a positive scalar controlling the squeezing of the network
mode	mode used for layout, either 'TL-tsne' or 'group-TL-tsne' (see attach_layout()). Default is 'TL-tsne'
vis_tool	a character indicating the visualisation tool, either 'ggnet' or visNetwork
edge_thrs	if non-null, a numeric (between 0 and 1) indicating an edge weight threshold for the representation
edge_diff_thrs	if non-null, a numeric (between 0 and 1) indicating an edge weight difference threshold under which edge weights of the two networks are considered equal
layout_metaweb	a boolean indicating whether the layout of the metaweb should be used to represent the difference network. to use metaweb layout = T, you need first to compute 'TL-tsne' layout for the metaweb for this beta value using attach_layout()
flip_coords	a boolean indicating whether coordinates should be flipped. In that case, y-axis is the trophic level and x-axis is the layout axis
alpha_per_group	controlling alpha per group (only for 'ggnet' vis), a list of format list(resolutions = "XX",groups = XX,alpha_focal = XX,alpha_hidden = XX), see example
alpha_per_node	controlling alpha per node (only for 'ggnet' vis), a list of format list(nodes = XX,alpha_focal = XX,alpha_hidden = XX), see example
TL_tsne.config	configuration list for mode 'TL-tsne', default is TL_tsne.default
nrep_ly	If several layouts for this beta value are attached to the metaweb (if layout_metaweb = T), index of the layout to use, see attach_layout()
ggnet.config	configuration list for ggnet representation, default is ggnet.default
visNetwork.config	configuration list for visNetwork representation, default is visNetwork.default

Value

an object of class ggplot or visNetwork, representation of the difference network

See Also

attach_layout()

Examples

#on Angola dataset
library(igraph)
library(metanetwork)

data(meta_angola)

diff_plot(g1 = meta_angola$X2003,g2 = meta_angola$X1986,metanetwork = meta_angola,
beta = 0.05)

MarcOhlmann/metanetwork documentation built on July 1, 2023, 6:27 a.m.