ziggurat_graph: Plotting a ziggurat graph

In jgalgarra/kcorebip: Bipartite networks kcore decomposition and visualization

Plotting a ziggurat graph

Description

This function plots the ziggurat graph of a bipartite network. Configuration parameters and results are stored in a global environment called zgg. 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 ziggurat_graph is called, zgg is destroyed and created again for the new plot. Plotting options are explained in the user manual.

Usage

ziggurat_graph(
  datadir,
  filename,
  style = "ziggurat",
  paintlinks = TRUE,
  print_to_file = FALSE,
  plotsdir = "plotresults/",
  orderkcoremaxby = "kradius",
  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,
  displace_y_b = rep(0, 20),
  displace_y_a = rep(0, 20),
  lsize_kcoremax = 3.5,
  lsize_zig = 3,
  lsize_kcore1 = 2.5,
  lsize_legend = 4,
  lsize_core_box = 2.5,
  labels_color = c(),
  height_box_y_expand = 1,
  kcore2tail_vertical_separation = 1,
  kcore1tail_disttocore = c(1, 1),
  innertail_vertical_separation = 1,
  factor_hop_x = 1,
  fattailjumphoriz = c(1, 1),
  fattailjumpvert = c(1, 1),
  coremax_triangle_height_factor = 1,
  coremax_triangle_width_factor = 1,
  paint_outsiders = TRUE,
  displace_outside_component = c(0, 0),
  outsiders_separation_expand = 1,
  outsiders_legend_expand = 1,
  specialistskcore2_horizontal_dist_rootleaf_expand = 1,
  specialistskcore2_vertical_dist_rootleaf_expand = 0,
  specialists_boxes_separation_count = 1,
  root_specialist_expand = c(1, 1),
  hide_plot_border = TRUE,
  rescale_plot_area = c(1, 1),
  kcore1specialists_leafs_vertical_separation = 1,
  corebox_border_size = 0.2,
  kcore_species_name_display = c(),
  kcore_species_name_break = c(),
  shorten_species_name = 0,
  exclude_species_number = FALSE,
  label_strguilda = "",
  label_strguildb = "",
  landscape_plot = TRUE,
  backg_color = "white",
  show_title = TRUE,
  show_legend = "BOTTOM",
  use_spline = TRUE,
  spline_points = 10,
  file_name_append = "",
  svg_scale_factor = 10,
  weighted_links = "none",
  square_nodes_size_scale = 1,
  move_all_SVG_up = 0,
  move_all_SVG_right = 0,
  progress = NULL
)

Arguments

datadir	the name of the file of the interaction matrix
filename	the file with the interaction matrix
style	equals 'ziggurat', do not modify
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
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
displace_y_b	relative vertical displacement of guild_b inner ziggurats
displace_y_a	relative vertical displacement of guild_a inner ziggurats
lsize_kcoremax	nodes in kshell max label size
lsize_zig	nodes in inner ziggurats label size
lsize_kcore1	labels of nodes in kshell 1
lsize_legend	legend label size
labels_color	default label colors
height_box_y_expand	expand inner ziggurat rectangles default height by this factor
kcore2tail_vertical_separation	expand vertical of kshell 1 species linked to kshell 2 by this factor
kcore1tail_disttocore	expand vertical separation of kshell 1 species from kshell max (guild_a, guild,b)
innertail_vertical_separation	expand vertical separation of kshell species connected to khsell > 2 & < kshell max
factor_hop_x	expand inner ziggurats horizontal distance
fattailjumphoriz	displace kshell 1 species linked to leftmost kshell max species
fattailjumpvert	idem for vertical position
coremax_triangle_height_factor	expand khsell max rectangles height by this factor
coremax_triangle_width_factor	expand khsell max rectangles width by this factor
paint_outsiders	paint species not connected to giant component
displace_outside_component	displace outsider species (horizontal, vertical)
outsiders_separation_expand	multiply by this factor outsiders' separation
outsiders_legend_expand	displace outsiders legend
specialistskcore2_horizontal_dist_rootleaf_expand	expand horizontal distance of specialist tail root node connected to kshell 2
specialistskcore2_vertical_dist_rootleaf_expand	expand vertical distance of specialist tails connected to kshell 2
specialists_boxes_separation_count	specialist species boxes separation count
root_specialist_expand	expand root specialist distances of tails connected to kshell <> 2
hide_plot_border	hide border around the plot
rescale_plot_area	full plot area rescaling (horizontal, vertical)
kcore1specialists_leafs_vertical_separation	expand vertical separation of specialist tails connected to kshell 1 species
corebox_border_size	width of kshell boxes
kcore_species_name_display	display species names of shells listed in this vector
kcore_species_name_break	allow new lines in species names of shells listed in this vector
shorten_species_name	number of characters of species name to display
exclude_species_number	do not include species number in species
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
use_spline	use splines to draw links
spline_points	number of points for each spline
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
move_all_SVG_up	move up all the SVG plot by this fraction, useful to crop upper white space
move_all_SVG_right	move rightwards all the SVG plot by this fraction, useful to crop right white space
progress	only for interactive apps, do not modifiy
lsize_kcorebox	default kshell boxes label size

Examples

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

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