plot difference network

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).

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

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)
#> mode is TL-tsne
#> plotting: X2003_Species - X1986_Species
#> mode is TL-tsne
#> beta = 0.05
#> Epoch: Iteration #100 error is: 907.373467955402
#> Epoch: Iteration #200 error is: 217.136794881583
#> Epoch: Iteration #300 error is: 217.265207284379
#> Registered S3 method overwritten by 'GGally':
#>   method from   
#>   +.gg   ggplot2

Arguments

Value

See also

Examples