Graph Plot

A function to plot a graph with nodes and edges.

Usage

GraphPlot(
  node,
  edge,
  transition = NULL,
  node_coord = c("x", "y"),
  node_group = NULL,
  node_palette = "Paired",
  node_palcolor = NULL,
  node_size = 4,
  node_alpha = 1,
  node_highlight = NULL,
  node_highlight_color = "red",
  label = FALSE,
  label.size = 3.5,
  label.fg = "white",
  label.bg = "black",
  label.bg.r = 0.1,
  label_insitu = FALSE,
  label_repel = FALSE,
  label_repulsion = 20,
  label_point_size = 1,
  label_point_color = "black",
  label_segment_color = "black",
  edge_threshold = 0.01,
  use_triangular = c("upper", "lower", "both"),
  edge_line = c("straight", "curved"),
  edge_line_curvature = 0.3,
  edge_line_angle = 90,
  edge_color = "grey40",
  edge_size = c(0.2, 1),
  edge_alpha = 0.5,
  edge_shorten = 0,
  edge_offset = 0,
  edge_highlight = NULL,
  edge_highlight_color = "red",
  transition_threshold = 0.01,
  transition_line = c("straight", "curved"),
  transition_line_curvature = 0.3,
  transition_line_angle = 90,
  transition_color = "black",
  transition_size = c(0.2, 1),
  transition_alpha = 1,
  transition_arrow_type = "closed",
  transition_arrow_angle = 20,
  transition_arrow_length = grid::unit(0.02, "npc"),
  transition_shorten = 0.05,
  transition_offset = 0,
  transition_highlight = NULL,
  transition_highlight_color = "red",
  aspect.ratio = 1,
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  legend.position = "right",
  legend.direction = "vertical",
  theme_use = "theme_scop",
  theme_args = list(),
  return_layer = FALSE
)

Arguments

node: A data frame representing the nodes of the graph.
edge: A matrix representing the edges of the graph.
transition: A matrix representing the transitions between nodes.
node_coord: A character vector specifying the names of the columns in node that represent the x and y coordinates.
node_group: A character vector specifying the name of the column in node that represents the grouping of the nodes.
node_palette: A character vector specifying the name of the color palette for node groups.
node_palcolor: A character vector specifying the names of the colors for each node group.
node_size: A numeric value or column name of node specifying the size of the nodes.
node_alpha: A numeric value or column name of node specifying the transparency of the nodes.
node_highlight: A character vector specifying the names of nodes to highlight.
node_highlight_color: A character vector specifying the color for highlighting nodes.
label: Whether to show labels for the nodes.
label.size: The size of the labels.
label.fg: A character vector specifying the foreground color of the labels.
label.bg: A character vector specifying the background color of the labels.
label.bg.r: The background color transparency of the labels.
label_insitu: Whether to display the node group labels in situ or as numeric values.
label_repel: Whether to use force-directed label repulsion.
label_repulsion: The repulsion force for labels.
label_point_size: The size of the label points.
label_point_color: A character vector specifying the color of the label points.
label_segment_color: A character vector specifying the color for the label segments.
edge_threshold: The threshold for removing edges.
use_triangular: A character vector specifying which part of the edge matrix to use (upper, lower, both).
edge_line: A character vector specifying the type of line for edges (straight, curved).
edge_line_curvature: The curvature of curved edges.
edge_line_angle: The angle of curved edges.
edge_color: A character vector specifying the color of the edges.
edge_size: A numeric vector specifying the range of edge sizes.
edge_alpha: The transparency of the edges.
edge_shorten: The length of the edge shorten.
edge_offset: The length of the edge offset.
edge_highlight: A character vector specifying the names of edges to highlight.
edge_highlight_color: A character vector specifying the color for highlighting edges.
transition_threshold: The threshold for removing transitions.
transition_line: A character vector specifying the type of line for transitions (straight, curved).
transition_line_curvature: The curvature of curved transitions.
transition_line_angle: The angle of curved transitions.
transition_color: A character vector specifying the color of the transitions.
transition_size: A numeric vector specifying the range of transition sizes.
transition_alpha: The transparency of the transitions.
transition_arrow_type: A character vector specifying the type of arrow for transitions (closed, open).
transition_arrow_angle: The angle of the transition arrow.
transition_arrow_length: The length of the transition arrow.
transition_shorten: The length of the transition shorten.
transition_offset: The length of the transition offset.
transition_highlight: A character vector specifying the names of transitions to highlight.
transition_highlight_color: A character vector specifying the color for highlighting transitions.
aspect.ratio: Aspect ratio of the panel. Default is 1.
title: The text for the title. Default is NULL.
subtitle: The text for the subtitle for the plot which will be displayed below the title. Default is NULL.
xlab: The x-axis label of the plot. Default is NULL.
ylab: The y-axis label of the plot. Default is NULL.
legend.position: The position of legends, one of "none", "left", "right", "bottom", "top". Default is "right".
legend.direction: The direction of the legend in the plot. Can be one of "vertical" or "horizontal".
theme_use: Theme used. Can be a character string or a theme function. Default is "theme_scop".
theme_args: Other arguments passed to the theme_use. Default is list().
return_layer: Whether to return the plot layers as a list. Defaults is FALSE.

Usage

Arguments

See also