Visualize a network with custom layouts

Usage

ggNetView(
  graph_obj,
  layout = NULL,
  node_add = 7,
  ring_n = NULL,
  r = 1,
  center = TRUE,
  idx = NULL,
  shrink = 1,
  k_nn = 12,
  push_others_delta = 0,
  layout.module = c("random", "adjacent", "order"),
  shape = 21,
  pointalpha = 1,
  pointsize = c(1, 10),
  pointstroke = 0.3,
  pointlabel = NULL,
  pointlabelsize = 5,
  group.by = "Modularity",
  fill.by = "Modularity",
  color.by = NULL,
  fill = NULL,
  color = NULL,
  jitter = FALSE,
  jitter_sd = 0.1,
  plot_line = TRUE,
  mapping_line = FALSE,
  curve = F,
  curvature = 0.25,
  linealpha = 0.25,
  linecolor = "grey70",
  label = FALSE,
  labelsize = 10,
  labelsegmentsize = 1,
  labelsegmentalpha = 1,
  add_group_outer = FALSE,
  add_group_outer_expand = 2,
  add_group_outer_color = "grey50",
  add_group_outer_fill = NULL,
  add_group_outer_fill_alpha = 0.2,
  add_group_outer_linetype = 1,
  add_group_outer_linewidth = 0.5,
  add_outer = FALSE,
  q_outer = 0.88,
  expand_outer = 1.02,
  outerwidth = 1.25,
  outerlinetype = 2,
  outeralpha = 0.5,
  nodelabsize = 5,
  remove = FALSE,
  dropOthers = FALSE,
  orientation = "up",
  angle = 0,
  scale = T,
  anchor_dist = 6,
  nrow = NULL,
  ncol = NULL,
  seed = 1115,
  scale_radius = NULL,
  return_layout = FALSE
)

Arguments

graph_obj: An graph object from build_graph_from_mat or build_graph_from_df. The network object to be visualized.
layout: Character string. Custom layouts; one of "gephi", "square", "square2", "petal", "petal2", "heart_centered","diamond", "star", "star_concentric","rectangle, "rightiso_layers" etc.
node_add: Integer (default = 7). Number of nodes to add in each layer of the layout.
ring_n: Numeric (default = 7) Numbers of ring in rings layout.
r: Numeric (default = 1). Radius increment for concentric or layered layouts.
center: Logical (default = TRUE). Whether to place a node at the center of the layout.
idx: Optional. Index of nodes to be emphasized or centered in the layout
shrink: Numeric (default = 1). Shrinkage factor applied to the center points.
k_nn: Numeric (default = 8). Number of nearest neighbors used to build the local adjacency graph.
push_others_delta: Numeric (default = 0). Radial offset applied to the "Others" module to slightly
layout.module: Character (default = "random") - adjacent : modules are positioned close to each other, minimizing inter-module gaps. - order : modules are distributed by order, applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout`
shape: Integer (default = 21). The point shape likely in ggplot2. If a character string is provided, it must be a variable name in graph_object for point shape mapping.
pointalpha: Integer (default = 1). The point alpha
pointsize: Vector (default = c(1,10)) The point size rang.
pointstroke: Integer (default = 0.3).
pointlabel: Character (default = NULL). Optional node label mode for top Degree nodes within each module. Supported values: "topN" (e.g. "top1", "top7", "top20") and "ALL".
pointlabelsize: Integer (default = 5). Change point label size.
group.by: Character (default = "Modularity"). Change group for nodes
fill.by: Character (default = "Modularity"). Change fill for nodes
color.by: Character (default = NULL). Change color for nodes. If provided, must be a variable name in graph_object. Numeric uses scale_color_gradient, otherwise uses scale_color_manual or scale_color_ggnetview.
fill: Named vector of colors for node fill (e.g. c("M1" = "red", "M2" = "blue")). If NULL (default), uses scale_fill_ggnetview; if provided, uses scale_fill_manual(values = fill).
color: Named vector of colors for node/edge/label color. If NULL (default), uses scale_color_ggnetview; if provided, uses scale_color_manual(values = color).
jitter: Logical (default = FALSE). Whether to apply jitter to points.
jitter_sd: Integer (default = 0.1). The standard deviation of the jitter applied when `jitter = TRUE`.
plot_line: Logical (default = TRUE). Whether to plot line in net plot.
mapping_line: Logical (default = FALSE). Whether to mapping line in ggNetView. If a character string is provided, it must be a variable name in graph_object for line color mapping.
curve: Logical (default = FALSE). Whether to plot curve line in net plot.
curvature: Integer (default = 0.25) The curve level of curve line when curve is TRUE
linealpha: Integer (default = 0.25). Change line alpha.
linecolor: Character (default = "grey70"). Change line color.
label: Logical or Character (default = FALSE). Controls module label text and module legend prefix. If FALSE, module text labels are not drawn and legend prefix uses "Modularity". If TRUE, module text labels are drawn and legend prefix uses "Modularity". If a character string, module text labels are drawn and that string is used as prefix for module text and module legend labels.
labelsize: Integer (default = 10). Change Module label size.
labelsegmentsize: Integer (default = 1). Change label segment size.
labelsegmentalpha: Integer (default = 1). Change label segment alpha.
add_group_outer: Logical (default = FALSE). Whether to add a circle boundary around the entire network (mimics ggforce::geom_mark_circle).
add_group_outer_expand: Numeric (default = 2). Expansion in mm for the group circle to account for point size; passed to geom_mark_circle(expand = ...).
add_group_outer_color: Character (default = "grey50"). Color of the group outer circle border.
add_group_outer_fill: Character or NULL (default = NULL). Fill color of the group outer circle. NULL = no fill (transparent).
add_group_outer_fill_alpha: Numeric (default = 0.2). Alpha (transparency) of the group outer circle fill; 0 = fully transparent, 1 = opaque.
add_group_outer_linetype: Integer or character (default = 1). Linetype of the group outer circle (e.g. 1 = solid, 2 = dashed).
add_group_outer_linewidth: Numeric (default = 0.5). Line width of the group outer circle.
add_outer: Logical (default = FALSE). Whether to add an outer circle/border around each module.
q_outer: Numeric (default = 0.88). Quantile of radial distance used to construct the smooth outer boundary for each module. Higher values make the boundary more expanded; lower values make it tighter.
expand_outer: Numeric (default = 1.02). Global scaling factor applied to the smoothed radial distances when drawing the outer boundary. Values > 1 slightly expand the boundary; values < 1 slightly shrink it.
outerwidth: Integer (default = 1.25). Change outer linewidth.
outerlinetype: Integer (default = 2). Change outer linetype.
outeralpha: Integer (default = 0.5). Change outer alpha.
nodelabsize: Integer (default = 5). Change node label size.
remove: Logical (default = FALSE). Remove "Others" only at the visualization stage (post-layout), so the layout of remaining modules is kept unchanged.
dropOthers: Logical (default = FALSE). If TRUE, remove nodes in the "Others" module from graph_obj before layout and visualization, then recompute layout/plot from the updated graph.
orientation: Character string. Custom orientation; one of "up","down","left","right".
angle: Integer (default = 0). Change orientation angle.
scale: Logical (default = T). modules applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout` to scale the radius
anchor_dist: Integer (default = 6) the distance of each modules, applicable to `Bipartite, Tripartite, Quadripartite, Multipartite, Pentapartite Layout`
nrow: Integer (default = NULL). the nrow of network with layout is "consensus_module_equal_gephi" or "consensus_module_gephi"
ncol: Integer (default = NULL). the ncol of network with layout is "consensus_module_equal_gephi" or "consensus_module_gephi"
seed: Integer (default = 1115). Random seed for reproducibility.
scale_radius: Numeric or NULL (default = NULL). When non-NULL, scale the layout so the network fits within this radius. Used by ggnetview_modularity_heatmaps for coordinate alignment.
return_layout: Logical (default = FALSE). When TRUE, return a list with $plot (ggplot) and $layout_data (graph_ly_final, graph_obj, ggplot_data, module_centroids) for downstream use (e.g. adding heatmaps and links).

Value

A ggplot object, or when return_layout = TRUE, a list with $plot and $layout_data.

Examples

NULL
#> NULL