ggmetanet

Function that provides network static representation (using 'ggnet') from a 'metanetwork' object using 'TL-tsne' or 'group-TL-tsne' layout.

ggmetanet(
  metanetwork,
  g = NULL,
  beta = 0.1,
  legend = NULL,
  mode = "TL-tsne",
  edge_thrs = NULL,
  layout_metaweb = FALSE,
  nrep_ly = 1,
  flip_coords = FALSE,
  diff_plot_bool = FALSE,
  alpha_per_group = NULL,
  alpha_per_node = NULL,
  alpha_interactive = FALSE,
  ggnet.config = ggnet.default,
  TL_tsne.config = TL_tsne.default
)

Arguments

metanetwork: object of class metanetwork
g: network (igraph object) to represent, default is metaweb
beta: the diffusion parameter of the diffusion kernel, a positive scalar controlling the vertical squeezing of the network
legend: resolution for the legend, legend resolution must be a coarser resolution than the resolution of g, default is NULL
mode: mode used for layout, 'TL-tsne' or 'group-TL-tsne' Default is 'TL-tsne'. This argument can also be a two-column matrix for custom layout.
edge_thrs: if non-null, a numeric (between 0 and 1) indicating an edge threshold for the representation
layout_metaweb: a boolean indicating whether the layout of the metaweb should be used to represent the network to use metaweb layout = TRUE, you need first to compute metaweb layout for this beta value using attach_layout()
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()
flip_coords: a boolean indicating whether coordinates should be flipped.
diff_plot_bool: boolean, do not edit by hand
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 In that case, y-axis is the trophic level and x-axis is the layout axis
alpha_interactive: a boolean indicating whether alpha (that is node transparency) should be asked in interactive mode to the user
ggnet.config: configuration list for ggnet representation, default is ggnet.default
TL_tsne.config: configuration list for mode 'TL-tsne', default is TL_tsne.default

Value

an object of class ggplot, the current network representation

Details

At each call of the function with 'TL-tsne' layout, it computes a layout for the current beta value. If a layout is already attached to the current network, it uses directly this layout (without computing). This function provides many static visualisation tools:

customising ggnet parameters wrapped in ggnet.config
legending using the trophicTable
playing on group transparency (alpha)
using the metaweb layout
building a legend for large networks.

Examples

library(metanetwork)
library(igraph)

#lattice example
g = make_lattice(dim = 2,length = 4,directed = TRUE)
#building metanetwork and computing trophic levels
meta0 = build_metanet(g) 
#> Warning: nodes of metaweb do not have names. Assigning integers as names
meta0 = compute_TL(meta0)
ggmetanet(meta0)
#> mode is TL-tsne
#> beta = 0.1
#> Epoch: Iteration #100 error is: 431.402455891932
#> Epoch: Iteration #200 error is: 101.980051220335
#> Epoch: Iteration #300 error is: 101.980051216652
#> Warning: node.size is invariant; size.cut ignored

#storing layout
meta0 = attach_layout(meta0)
#> attaching TL-tsne layout for metaweb_
#> 
#>                   beta = 0.1
#> beta = 0.1
#> Epoch: Iteration #100 error is: 431.402455891914
#> Epoch: Iteration #200 error is: 101.980051214718
#> Epoch: Iteration #300 error is: 101.980051216652
ggmetanet(meta0)
#> mode is TL-tsne
#> Warning: node.size is invariant; size.cut ignored


#custom ggnet parameters
ggnet.custom = ggnet.default
ggnet.custom$label = TRUE
ggnet.custom$edge.alpha = 0.5
ggnet.custom$alpha = 0.7
ggnet.custom$arrow.size = 1
ggnet.custom$max_size = 12

# using pre-computed layout and custom ggnet parametersfor vertebrates metaweb
data("meta_vrtb")
#custom ggnet parameters
ggnet.custom = ggnet.default
ggnet.custom$label = TRUE
ggnet.custom$edge.alpha = 0.5
ggnet.custom$alpha = 0.7
ggnet.custom$arrow.size = 1
ggnet.custom$max_size = 12
#at SBM group level
beta = 0.005
ggmetanet(meta_vrtb,g = meta_vrtb$metaweb_group,flip_coords = TRUE,
         beta = beta,legend = "group",
         ggnet.config = ggnet.custom,edge_thrs = 0.1)
#> mode is TL-tsne
#> too many groups, assigning colors and shapes

Arguments

Value

Details

See also

Examples