bipartite_graph: Plotting a bipartite graph

In jgalgarra/kcorebip: Bipartite networks kcore decomposition and visualization

Plotting a bipartite graph

Description

This function plots the ziggurat graph of a bipartite network. Configuration parameters and results are stored in a global environment called bpp. This environment is not destroyed after the function is executed, so the developer can store it in a configuration file, retrieve network analysis variables and so on. If a new bipartite_graph is called, bpp is destroyed and created again for the new plot. Plotting options are explained in the user manual.

Usage

bipartite_graph(
  datadir,
  filename,
  paintlinks = TRUE,
  print_to_file = FALSE,
  plotsdir = "plot_results/",
  orderkcoremaxby = "kradius",
  style = "legacy",
  guild_gap_increase = 1,
  flip_results = FALSE,
  aspect_ratio = 1,
  alpha_level = 0.2,
  color_guild_a = c("#4169E1", "#00008B"),
  color_guild_b = c("#F08080", "#FF0000"),
  color_link = "slategray3",
  alpha_link = 0.5,
  size_link = 0.5,
  lsize_kcoremax = 3,
  lsize_kcore1 = 2.5,
  lsize_legend = 4,
  lsize_core_box = 2.5,
  labels_color = c(),
  hide_plot_border = TRUE,
  corebox_border_size = 0.2,
  label_strguilda = "",
  label_strguildb = "",
  landscape_plot = TRUE,
  backg_color = "white",
  show_title = TRUE,
  show_legend = "TOP",
  file_name_append = "",
  svg_scale_factor = 10,
  weighted_links = "none",
  square_nodes_size_scale = 1,
  zoom_svgplot = 1,
  progress = NULL
)

Arguments

datadir	the name of the file of the interaction matrix
filename	the file with the interaction matrix
print_to_file	if set to FALSE the plot is displayed in the R session window
plotsdir	the directory where the plot is stored
orderkcoremaxby	sets order of kcoremax nodes, by kradius or kdegree
style	bipartite representation style: legacy, kcoreorder, chilopod
guild_gap_increase	controls the disptance between guild rows
flip_results	displays the graph in portrait configuration
aspect_ratio	ziggurat plot default aspect ratio
alpha_level	transparency for ziggurats' filling
color_guild_a	default filling for nodes of guild_a
color_guild_b	default filling for nodes of guild_b
color_link	default links color
alpha_link	link transparency
size_link	width of the links
lsize_kcoremax	nodes in kshell max label size
lsize_legend	legend label size
labels_color	default label colors
hide_plot_border	hide border around the plot
corebox_border_size	width of kshell boxes
label_strguilda	string labels of guild a
label_strguildb	string labels of guild b
landscape_plot	paper landscape configuration
backg_color	plot background color
show_title	show plot title
show_legend	show plot legend position
file_name_append	a label that the user may append to the plot file name for convenience
svg_scale_factor	only for interactive apps, do not modify
weighted_links	function to add link weight: 'none', 'log10' , 'ln', 'sqrt'
square_nodes_size_scale	scale nodes area of kcore1 and outsiders
zoom_svgplot	scale SVG plot, just for interactive applications
progress	only for interactive apps, do not modifiy

Examples

bipartite_graph("data/","M_PL_001.csv",plotsdir="grafresults/",print_to_file = TRUE)

jgalgarra/kcorebip documentation built on June 14, 2025, 12:33 a.m.