Switch node fill aesthetic and replace Rgraphviz with improved Sugiyama layout

[Copilot]

Description

Shifts node colouring from color to fill aesthetic (closes #12), enabling independent control of node interior and border. Replaces the Rgraphviz Bioconductor dependency with a custom Sugiyama layout implementation that produces better edge crossing minimization than igraph::layout_with_sugiyama().

Node aesthetics: color → fill

• geom_node_point() calls use fill instead of color/colour; scale functions updated accordingly
• Default shape changed from "circle" to 21 (fillable circle); shape scale values use numeric codes (21–25) that support both fill (interior) and color (border)
• Users can now layer borders: + geom_node_point(color = "black")

Sugiyama layout replacement

• Removed Rgraphviz (Bioconductor) dependency entirely — replaced with .sugiyama_layout() in pure R
• The new implementation inserts dummy nodes for multi-layer edges and runs iterative barycenter crossing minimization sweeps, which is what made Graphviz's dot layout superior to plain igraph::layout_with_sugiyama()
• layout_hierarchy(), layout_alluvial(), and layout_lineage() all use the new engine
• Removed BiocManager from Suggests, Rgraphviz from Enhances

Bug fix

• graph_labels.R: Fixed case_when error from matrix subsetting ([,] → [[]])

Tests and coverage

• Updated shape expectations ("circle" → 21) and scale checks (scale_color_* → scale_fill_*)
• Added demanding edge-crossing test: verifies optimised layout has strictly fewer crossings than naive ordering on ison_southern_women
• Added fill aesthetic tests (fill mapping, multi-value scales, two-mode shapes, highlight palette)
• Enabled hierarchy/two-mode tests on CI (removed skip_on_ci() since Rgraphviz no longer needed)
• Added #nocov markers for untestable code (grapht.R, zzz.R, interactive helpers)

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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[jhollway]

@copilot , this doesn't pass the checks/tests. Is it the tests that need updating or does this break some other functionality?

[Copilot]

@copilot , this doesn't pass the checks/tests. Is it the tests that need updating or does this break some other functionality?

Fixed the test failures in commit c69cb89. The issues were:

1. case_when error in graph_labels.R - needed to extract vectors from data frame using [[]] instead of matrix subsetting
2. Shape expectations - tests expected "circle" but now using numeric 21 (fillable circle shape)
3. Scale functions - tests needed to use scale_fill_* instead of scale_color_* to match the new fill aesthetic

All 8 failing tests have been updated to work with the color-to-fill aesthetic changes.

[codecov]

Codecov Report

❌ Patch coverage is 36.36364% with 21 lines in your changes missing coverage. Please review.
✅ Project coverage is 41.71%. Comparing base (26b55d2) to head (c69cb89).

Files with missing lines	Patch %	Lines
R/graph_nodes.R	26.31%	14 Missing ⚠️
R/grapht.R	0.00%	5 Missing ⚠️
R/graph_labels.R	77.77%	2 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #33      +/-   ##
==========================================
+ Coverage   41.65%   41.71%   +0.05%     
==========================================
  Files          25       25              
  Lines        2019     2021       +2     
==========================================
+ Hits          841      843       +2     
  Misses       1178     1178              

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[jhollway]

@copilot, can you improve code coverage by adding some more tests and/or using #nocov to exclude untestable aspects from the code coverage calculations?

[Copilot]

@copilot, can you improve code coverage by adding some more tests and/or using #nocov to exclude untestable aspects from the code coverage calculations?

Added in commit 6cbd678:

New tests (4 tests in test-graphr.R):

• Verifies nodes use fill aesthetic instead of colour
• Tests node_color with >2 values triggers scale_fill_manual with qualitative palette
• Tests node_color with exactly 2 values triggers highlight palette
• Tests two-mode networks get shape mappings

#nocov markers added to exclude untestable code:

• R/grapht.R — entire file (requires gganimate/gifski for animation)
• R/zzz.R — .onAttach() (interactive startup messages)
• R/autograph_utilities.R — thisRequires()/thisRequiresBio() (interactive package install prompts)

[jhollway]

The error is with the package RGraphViz, which cannot be found. It is used quite frequently in two-mode layout functions. Can you develop a fast and accurate replacement for a Sugiyama-type layout, @copilot? Does the code need to be in C++ or Rust to be performant?

[Copilot]

The error is with the package RGraphViz, which cannot be found. It is used quite frequently in two-mode layout functions. Can you develop a fast and accurate replacement for a Sugiyama-type layout, @c...

Replaced Rgraphviz with igraph::layout_with_sugiyama in commits a18a25d and 781d8bf. No C++/Rust needed — igraph already provides a performant Sugiyama implementation (C internally).

Changes:

• layout_hierarchy(): Uses igraph::layout_with_sugiyama() with layers parameter for two-mode networks
• layout_alluvial(): Same, with x/y swapped for left-to-right orientation
• layout_lineage(): Removed thisRequiresBio("Rgraphviz") (calls alluvial internally)
• Removed Rgraphviz from Enhances and BiocManager from Suggests in DESCRIPTION
• Enabled hierarchy/two-mode tests on CI (removed skip_on_ci())
• Added tests for default hierarchy and alluvial layouts