Plotting lineage tree - #320
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Add plot_lineage_tree in tracksdata.functional._plot: render lineage trees with matplotlib, supporting attribute-bound node colors and sizes, time windows, and exact timestamps. Export from tracksdata.functional and add an optional `plot` extra (matplotlib). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
…lineage_tree Rename color_attr/size_attr to color/size and let color, size, marker, and text each accept either a fixed value or a callable resolving a per-node value from the node's attribute row: - color: numeric attr or callable returning numbers -> cmap + colorbar; callable returning literal colors (names/hex/RGBA) -> used verbatim. - size: attr mapped to size_range, callable returning raw sizes, or constant. - marker: single glyph, or callable returning a per-node glyph (nodes are grouped by glyph, one scatter call per group, sharing one normalization). - text: attr name or callable -> per-node annotation, styled via text_kwargs. Add `attrs` to declare the node keys callables read. If a callable is given without `attrs`, warn and load all node attributes (may pull mask blobs). Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Co-Authored-By: Claude Opus 5 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WwHX5ciJfQPm9z6zmBsb27
yfukai
marked this pull request as ready for review
September 10, 2026 01:06
…ature - add `edge_color`, resolved like `color` (attribute name, callable, or literal color); numeric edge values share `cmap`/`color_norm` with the face color and are mapped manually since scatter only colormaps `c` - a `color`/`edge_color` string that is not a node attribute is taken as a literal matplotlib color (previously a ValueError) - drop `node_size`: `size` now defaults to 30.0 and accepts a float - drop `time_range`: `time_points=range(a, b + 1)` covers it Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WwHX5ciJfQPm9z6zmBsb27
- resolve requested attribute keys through a single validation path and dedupe with dict.fromkeys; typos in `size`/`text` now raise ValueError even when a callable triggers loading all attributes - fold `_resolve_color_values` into `_resolve_color_channel` - draw every marker glyph through one grouped scatter loop, inlining the former `_scatter_group` closure; scalar sizes are expanded to an array so `size` consistently overrides `scatter_kwargs["s"]` - build the successor adjacency with a polars group_by and look up node coordinates with `Series.replace_strict` - compute the orientation flag once and label the time axis via `Axis.set_label_text` - rename the shadowed `time_points` local to `shown_time_points` Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WwHX5ciJfQPm9z6zmBsb27
- `time_points` now only limits where markers are drawn; edges are drawn for every node between the first and last displayed time point, so divisions stay at their true time instead of being bridged - with `time_positions=None`, all time points in the displayed range are evenly separated (hidden ones included) and only the displayed ones are labeled - build edge segments with two polars joins on node coordinates and drop the `_bridged_edge_segments` walk - map attribute sizes with `matplotlib.colors.Normalize(clip=True)` instead of `_map_to_size_range`; `size_norm` also accepts a `Normalize` instance, mirroring `color_norm` Co-Authored-By: Claude Fable 5.1 <noreply@anthropic.com> Claude-Session: https://claude.ai/code/session_01WwHX5ciJfQPm9z6zmBsb27
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Plotting lineage trees of tracksdata in matplotlib. I believe this is of interest to a fraction of users!