v0.6.0

[Copilot]

Adds isolate handling, fill-based node aesthetics, and removes the Bioconductor ({Rgraphviz}) dependency for Sugiyama layouts. NEWS.md updated to document all changes.

Graphing

• Added isolates argument to graphr(): "legend" (default), "caption", or "keep" — removes isolates from layout while optionally annotating them (closes Rely on fill instead of color for graphr/s/t functions for flexibility and consistency #12)
• graphr() now auto-dispatches to graphs() when passed a list of graphs
• graphs() no longer requires {patchwork} to be loaded separately
• Changed node aesthetics from color to fill using fillable shape codes (21–25)
• Consolidated legend modifications into internal graph_legends() helper
• Improved legend labelling: "Sign", "Weight"/"Width", "Mode"/"Shape"

Layouts

• Replaced {Rgraphviz} (Bioconductor) with igraph::layout_with_sugiyama, removing the Bioconductor dependency
• Improved Sugiyama layout with dummy node insertion and barycenter crossing minimisation

Package

• Updated logo

Checklist:

• Documentation
  • DESCRIPTION file version is bumped by the appropriate increment (major, minor, patch)
  • Date in DESCRIPTION is correct
  • Longer functions are commented inline or broken down into helper functions to help debugging
• PR form
  • Title indicates expected version number
  • PR description above and the NEWS.md file are aligned
  • Description above itemizes changes under subsection titles, e.g. "## Data"
  • Closed, fixed, or related issues are referenced and explained in the description above, e.g. "Fixed #0 by adding A"

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