NetworkAtomic: NetworkAtomic

In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

NetworkAtomic

Description

Core implementation for rendering a single network graph from a links (edge list) data frame and an optional nodes (vertex metadata) data frame. This is the workhorse behind the exported Network function – it takes a single pair of links/nodes data frames (no split_by support) and returns a ggplot object.

The graph is constructed via graph_from_data_frame, laid out using igraph layout algorithms ("circle", "tree", "grid", or any named igraph layout such as "fr" or "kk"), and rendered with ggraph using geom_edge_arc for links and geom_point for nodes.

Key features include:

• Directed / undirected graphs with optional arrow heads.

• Link styling: variable width (weight), linetype, and colour, each constant or mapped from a column. Edge colours can follow source nodes, target nodes, or a dedicated column.

• Node styling: variable size, shape, colour, and fill, each constant or column-mapped.

• Community detection via igraph clustering algorithms with convex hull, ellipse, rectangle, or circle marks from ggforce.

• Automatic labels via geom_text_repel.

• Self-loop edges drawn as direction-sensitive arcs.

Usage

NetworkAtomic(
  links,
  nodes = NULL,
  from = NULL,
  from_sep = "_",
  to = NULL,
  to_sep = "_",
  node_by = NULL,
  node_by_sep = "_",
  link_weight_by = 2,
  link_weight_name = NULL,
  link_type_by = "solid",
  link_type_name = NULL,
  node_size_by = 15,
  node_size_name = NULL,
  node_color_by = "black",
  node_color_name = NULL,
  node_shape_by = 21,
  node_shape_name = NULL,
  node_fill_by = "grey20",
  node_fill_name = NULL,
  link_alpha = 1,
  node_alpha = 0.95,
  node_stroke = 1.5,
  cluster_scale = c("fill", "color", "shape"),
  node_size_range = c(5, 20),
  link_weight_range = c(0.5, 5),
  link_arrow_offset = 20,
  link_curvature = 0,
  link_color_by = "from",
  link_color_name = NULL,
  palette = "Paired",
  palcolor = NULL,
  palreverse = FALSE,
  link_palette = ifelse(link_color_by %in% c("from", "to"), palette, "Set1"),
  link_palcolor = if (link_color_by %in% c("from", "to")) palcolor else NULL,
  directed = TRUE,
  layout = "circle",
  cluster = "none",
  add_mark = FALSE,
  mark_expand = ggplot2::unit(10, "mm"),
  mark_type = c("hull", "ellipse", "rect", "circle"),
  mark_alpha = 0.1,
  mark_linetype = 1,
  add_label = TRUE,
  label_size = 3,
  label_fg = "white",
  label_bg = "black",
  label_bg_r = 0.1,
  arrow = ggplot2::arrow(type = "closed", length = ggplot2::unit(0.1, "inches")),
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  aspect.ratio = 1,
  theme = "theme_this",
  theme_args = list(),
  legend.position = "right",
  legend.direction = "vertical",
  ...
)

Arguments

links	A data frame containing the edge list. Must contain the from and to columns specifying source and target node identifiers. Additional columns can be referenced by other parameters (e.g., link_weight_by, link_type_by, link_color_by).
nodes	An optional data frame of node metadata. When provided, columns such as node_size_by, node_color_by, node_shape_by, and node_fill_by can reference its columns. When NULL, the node set is inferred from the unique values in the from and to columns. If a single character string starting with "@", the nodes data frame is extracted from the corresponding attribute of links (e.g. "@nodes" extracts attr(links, "nodes")).
from	A character string specifying the column name in links for the source node identifiers. Defaults to "from", or the first column of links if that column name does not exist. Multiple columns can be provided; they are concatenated with from_sep.
from_sep	A character string to join multiple from columns. Default "_". Ignored when from is a single column.
to	A character string specifying the column name in links for the target node identifiers. Defaults to "to", or the second column of links if that column name does not exist. Multiple columns can be provided; they are concatenated with to_sep.
to_sep	A character string to join multiple to columns. Default "_". Ignored when to is a single column.
node_by	A character string specifying the column name in nodes for the node identifiers. These must match the values in the from / to columns of links. Defaults to "name", or the first column of nodes if that column name does not exist. Multiple columns can be provided; they are concatenated with node_by_sep.
node_by_sep	A character string to join multiple node_by columns. Default "_". Ignored when node_by is a single column.
link_weight_by	A numeric value or a character string. If numeric, all edges receive that constant line width. If a column name, the edge line width is mapped to that column. Default 2.
link_weight_name	A character string for the link weight legend title. When NULL (default), the column name from link_weight_by is used. Only relevant when link_weight_by is a column name.
link_type_by	A character string or a column name specifying the edge linetype. Can be "solid", "dashed", "dotted", etc. If a column name from links is supplied, the linetype is mapped to that column (with a version check for ggplot2 4.0.0, where mapping is unsupported and a warning is issued). Default "solid".
link_type_name	A character string for the link linetype legend title. When NULL (default), the column name from link_type_by is used. Only relevant when link_type_by is a column name.
node_size_by	A numeric value or a character string. If numeric, all nodes receive that constant point size. If a column name, the size is mapped to that column. Default 15.
node_size_name	A character string for the node size legend title. When NULL (default), the column name from node_size_by is used. Only relevant when node_size_by is a column name.
node_color_by	A character string specifying the node colour. If a colour name or hex code (e.g. "black"), all nodes receive that constant colour. If a column name from nodes is supplied, the colour is mapped to that column. Default "black".
node_color_name	A character string for the node colour legend title. When NULL (default), the column name from node_color_by is used. Only relevant when node_color_by is a column name.
node_shape_by	A numeric value or a character string. If numeric, all nodes receive that constant shape (see shape). If a column name, the shape is mapped to that column (cast to factor). Default 21 (filled circle with border).
node_shape_name	A character string for the node shape legend title. When NULL (default), the column name from node_shape_by is used. Only relevant when node_shape_by is a column name.
node_fill_by	A character string specifying the node fill colour. If a colour name or hex code (e.g. "grey20"), all nodes receive that constant fill. If a column name from nodes is supplied, the fill is mapped to that column. Default "grey20".
node_fill_name	A character string for the node fill legend title. When NULL (default), the column name from node_fill_by is used. Only relevant when node_fill_by is a column name.
link_alpha	A numeric value specifying the transparency (alpha) of the edge lines. Between 0 (invisible) and 1 (opaque). Default 1.
node_alpha	A numeric value specifying the fill transparency of the nodes. Only applies when node_shape_by is one of the filled shapes (21–25). Default 0.95.
node_stroke	A numeric value specifying the border stroke width of the node points. Default 1.5.
cluster_scale	A character string specifying which node aesthetic is overridden by cluster membership. One of "fill", "color", or "shape". The value is matched via match.arg; default is "fill".
node_size_range	A numeric vector of length 2 giving the minimum and maximum node size (in ggplot2 point units) when node_size_by is a column name. Default c(5, 20).
link_weight_range	A numeric vector of length 2 giving the minimum and maximum edge line width (in mm) when link_weight_by is a column name. Default c(0.5, 5).
link_arrow_offset	A numeric value (in points) specifying the offset distance for the arrow end cap from the target node. Prevents arrow heads from overlapping the node points. Only relevant when directed = TRUE. Default 20.
link_curvature	A numeric value controlling the curvature of the edges. 0 (default) produces straight edges; positive values curve them away from the direct path.
link_color_by	A character string controlling how edge colour is determined. Options: "from" (default) – colour follows the source node's fill or colour aesthetic. "to" – colour follows the target node's fill or colour. A column name from links – colour is mapped directly to that column.
link_color_name	A character string for the edge colour legend title. Only used when link_color_by is a column name (not "from" or "to"). When NULL (default), the column name is used.
palette	A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.
palcolor	A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).
palreverse	A logical value indicating whether to reverse the palette. Default is FALSE.
link_palette	A character string specifying the palette for edge colours when they are mapped. When link_color_by is "from" or "to", defaults to the node palette. Otherwise defaults to "Set1".
link_palcolor	A character vector specifying custom colours for the edge palette. When link_color_by is "from" or "to", defaults to the node palcolor. Otherwise defaults to NULL.
directed	A logical value. When TRUE, edges are drawn with arrow heads and an end-cap offset. Default TRUE.
layout	A character string or an igraph_layout_spec object specifying the node placement algorithm. Built-in shortcuts: "circle" (circular layout), "tree" (hierarchical tree), "grid" (grid layout). Any other string is prefixed with "layout_with_" and called as an igraph function (e.g. "fr" for Fruchterman–Reingold, "kk" for Kamada–Kawai). Default "circle".
cluster	A character string specifying the community detection algorithm. One of "none", "fast_greedy", "walktrap", "edge_betweenness", "infomap", or a custom clustering function from igraph. When not "none", cluster membership overrides the aesthetic selected by cluster_scale. Default "none".
add_mark	A logical value. When TRUE (and cluster != "none"), an enclosure mark is drawn around each cluster's nodes. Default FALSE.
mark_expand	A unit object specifying the extra space around points within a cluster mark. Default unit(10, "mm").
mark_type	A character string specifying the mark geometry. One of "hull", "ellipse", "rect", or "circle", corresponding to ggforce's geom_mark_hull, geom_mark_ellipse, geom_mark_rect, and geom_mark_circle. The value is matched via match.arg; default is "hull".
mark_alpha	A numeric value for the fill transparency of cluster marks. Default 0.1.
mark_linetype	A numeric or character value specifying the border line type of the cluster marks. Default 1 (solid).
add_label	A logical value. When TRUE (default), node identifiers are drawn as repulsive text labels via geom_text_repel.
label_size	A numeric value for the font size of node labels. Scaled by the theme base size. Default 3.
label_fg	A character string specifying the text colour of node labels. Default "white".
label_bg	A character string specifying the background colour of node labels. Default "black".
label_bg_r	A numeric value specifying the background box radius (as a fraction of label height). Passed to geom_text_repel's bg.r argument. Default 0.1.
arrow	A arrow object for the link arrow heads. Only used when directed = TRUE. Default is arrow(type = "closed", length = unit(0.1, "inches")).
title	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
subtitle	A character string specifying the subtitle of the plot.
xlab	A character string specifying the x-axis label.
ylab	A character string specifying the y-axis label.
aspect.ratio	A numeric value specifying the aspect ratio of the plot.
theme	A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
theme_args	A list of arguments to pass to the theme function.
legend.position	A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".
legend.direction	A character string specifying the direction of the legend.
...	Not used.

Value

A ggplot object with height and width attributes (in inches).

Architecture

1. Column resolution – Default column names for from, to, and node_by are assigned when NULL, using the first or second column of the respective data frame. Each is validated via check_columns; multi-column inputs are concatenated with their respective separator (from_sep, to_sep, node_by_sep) and force-converted to factors. Resolved columns are renamed to the canonical names "from", "to", and "name".

2. Graph construction – An igraph object is built via graph_from_data_frame using the links data frame and (optionally) the nodes data frame. If nodes is a string starting with "@", it is extracted from the corresponding attribute on the links object.

3. Layout computation – The layout is resolved: "circle" -> layout_in_circle, "tree" -> layout_as_tree, "grid" -> layout_on_grid. Any other character string is prefixed with "layout_with_" and looked up in the igraph namespace (e.g. "fr" -> layout_with_fr). If layout is already an igraph_layout_spec object it is applied directly via layout_.

4. Data extraction – Vertex and edge data frames are extracted from the igraph object via as_data_frame. Layout coordinates are added as x and y columns to the vertex data.

5. Node aesthetic assembly – Each of size, color, shape, and fill is resolved as either a constant value (numeric or character) or a mapping to a column of the node data. A per-aesthetic "guide" / "none" flag is tracked for legend construction.

6. Link aesthetic assembly – linewidth (weight), linetype, and color are resolved similarly.

   • When link_color_by = "from", edge colours are derived from the source node's fill (if node shape is filled, 21–25) or colour; when "to", from the target node.

   • When link_color_by names a column in the links data frame (other than "from"/"to"), it is mapped directly.

   If directed = TRUE, a arrow is added and end_cap is set via circle to prevent arrow overlap with nodes. Self-loop edges receive a direction aesthetic.

7. Plot initialisation – A ggraph plot is created with layout = "manual" and vertex coordinates from the layout.

8. Clustering and marks – When cluster != "none", the specified igraph community-detection algorithm is run (cluster_fast_greedy, cluster_walktrap, cluster_edge_betweenness, cluster_infomap, or a custom function). Membership overrides the aesthetic specified by cluster_scale ("fill", "color", or "shape") with a warning that the previous setting is discarded. If add_mark = TRUE, a mark enclosure (hull / ellipse / rect / circle) is drawn per cluster via the corresponding ggforce geom.

9. Link rendering – geom_edge_arc draws the edges (with configurable link_curvature) and geom_edge_loop handles self-loop edges.

10. Link scales – Conditional on their guide status, scale_edge_width_continuous, scale_edge_linetype_discrete, and scale_edge_color_manual / scale_edge_color_gradientn are added for weight, linetype, and colour legends respectively.

11. Node rendering – geom_point draws the nodes with the assembled aesthetics.

12. Node scales – Conditional scale additions: scale_size_continuous (range from node_size_range), scale_color_manual, scale_shape_manual, and scale_fill_manual, each with their legend title and guide overrides.

13. Labels – When add_label = TRUE, node identifiers are rendered via geom_text_repel using label_fg, label_bg, and label_bg_r.

14. Final theme and dimensions – Coordinate expansion, axis labels, theme application, and legend positioning are applied. Plot height and width are computed via calculate_plot_dimensions and stored as attributes.

plotthis documentation built on July 9, 2026, 5:07 p.m.