ggmetanet: ggmetanet
In metanetwork: Handling and Representing Trophic Networks in Space and Time

ggmetanet

R Documentation

ggmetanet

Description

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

Usage

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

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.

Value

an object of class ggplot, the current network representation

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) 
meta0 = compute_TL(meta0)
ggmetanet(meta0)
#storing layout
meta0 = attach_layout(meta0)
ggmetanet(meta0)

#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)

metanetwork documentation built on Dec. 5, 2022, 5:22 p.m.