Interactive plots for Rsim — webplotviz • rpathviz

Interactive plots for Rsim plot using plotly:: package and tidyverse::

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Usage

webplotviz(
  Rpath.obj,
  eco.name = attr(Rpath.obj, "eco.name"),
  line.col = "grey",
  h_spacing = 3,
  node_size_min = 1,
  node_size_max = 30,
  fleet_color = "#B40F20",
  groups_palette = "rpath_pal_dark",
  text_size = 3,
  max.overlaps = 50,
  gradient = TRUE,
  labels = TRUE,
  cluster_method = c("fast_greedy", "louvain", "walktrap", "edge_betweenness")
)

Arguments

Rpath.obj: An object of class Rpath rpath().
eco.name: Optional name of the ecosystem. Default is the eco.name attribute from the rpath object created from running rpath().
line.col: description.
h_spacing: horizontal spacing multiplier, it spreads nodes horizontally.
node_size_min: from scale_value() Minimum value of the new scale (default is 1).
node_size_max: from scale_value() Maximum value of the new scale (default is 30).
fleet_color: single color for fleet nodes.
groups_palette: color palette for non-fleet groups. Two palette options rpath_pal_dark and rpath_pal_light.
text_size: size of the text labels.
max.overlaps: maximum number of overlapping labels allowed by ggrepel. Increase for denser label coverage, decrease to reduce clutter. Default is 50.
gradient: Logical. If TRUE(default), edges are drawn with a colour gradient (prey-to-predator) using after_stat(index). If FALSE, edges are drawn in a fixed line.col colour, which renders significantly faster for large food webs.
labels: Logical. If TRUE (default), group names are drawn using ggrepel to avoid overlap. Set to FALSE to skip labels entirely, which roughly halves render time on large food webs.
cluster_method: Community detection algorithm used to colour node clusters. One of "fast_greedy" (default), "louvain", "walktrap", or "edge_betweenness". "fast_greedy" and "louvain" are recommended for large food webs; "edge_betweenness" is the most accurate but significantly slower.

Value

Returns a plot visualization of the food web.

Contributors

webplot original function from Rpath by Kerim Aydin

Plotting

Caution: For large food webs see the examples.

Examples

if (FALSE) { # \dontrun{
# Read in Rpath parameter file, generate and name model object
Rpath.obj <- Rpath::rpath(Rpath::AB.params, eco.name = "Anchovy Bay")
# Plot food web diagram with all groups labeled, including fleets
webplotviz(Rpath.obj, h_spacing = 3, text_size = 3)

# For large food webs, use labels = FALSE to speed up rendering, then save
# with ggsave() for best results.
# 1) assign the plot to an object
# 2) use ggplot2::ggsave() to save the plot for a fast visualization
Rpath.obj <- Rpath::rpath(Rpath::Ecosense.EBS, eco.name = "Eastern Bering Sea")
wp <- webplotviz(Rpath.obj, h_spacing = 3, text_size = 3,
  node_size_min = 1, node_size_max = 50, labels = FALSE)
ggplot2::ggsave("figures/EBSfoodwebplot2.png", wp, width = 16, height = 10)


} # }