scverse / scverse/spatialdata-plot
Additive RGB color blending for render_shapes / render_labels (and render_points)
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描述
Motivation
Spun out from #321 (the thread there mixes two unrelated asks — this issue is the second one, originally raised by @brainfo).
`render_images` already supports multi-channel additive compositing: you pass several channels with per-channel colormaps and they blend into a single RGB image, mirroring napari / ImageJ / FIJI for fluorescence microscopy. The same idiom is useful for sequencing-based spatial data, where a user wants to visualize co-expression of 2–3 genes per cell/spot/region on a single axis — red for gene A, green for gene B, blue for gene C, additively blended so co-expressing cells appear yellow/cyan/white.
Today this requires manual post-processing (the user in #321 mentions doing it in Illustrator).
Proposed API
Mirror the existing `render_images` multi-channel convention by letting `color` accept a list of obs/var columns on `render_shapes`, `render_labels`, and `render_points`:
```python
sdata.pl.render_shapes(
color=["Sox2", "Pax6", "Tbr2"],
palette=["red", "green", "blue"], # one color per channel
channels_as_legend=True,
).pl.show()
sdata.pl.render_labels(
color=["Sox2", "Pax6"],
palette=["red", "green"],
).pl.show()
sdata.pl.render_points(
color=["Sox2", "Pax6"],
).pl.show()
```
Output: a single axis (no multi-panel grid). Each shape / label / point gets one composited color derived from its per-column values blended via per-channel colormaps, identical in spirit to the additive multi-channel path already in `render_images`.
Why this is feasible
- The additive-blending machinery already exists in `pl/render.py` for the multi-channel image path (see `render_images` branches 2A/2B/2C). The same per-channel cmap + sum + clip logic applies.
- Single-axis output sidesteps the hierarchy-of-axes complexity that made multi-panel `color=[...]` (the other ask from #321) undesirable.
- `channels_as_legend` already exists for `render_images`; can extend.
Scope
- In scope: 2–3-column color lists on `render_shapes`, `render_labels`, `render_points`. Per-channel `cmap` or `palette`. Additive blend on a single axis.
- Out of scope (defer or decline):
- Multi-panel grids (`sc.pl.umap`-style) — already declined in #321.
- Arbitrary blend modes beyond additive — start with the existing `render_images` semantics.
- PCA-based or learned color reductions for >3 channels.
Edge cases to design for
- Length mismatch between `color` list and `palette` list.
- Mixing categorical and continuous columns in the same `color` list (probably reject with a clear error).
- NaN handling per column (skip vs zero vs error — likely error, matching the recent `render_images` NaN rejection).
- Per-column `norm` / `vmin` / `vmax` — accept a list, parallel to the per-channel `norm` already supported on `render_images`.
- `groups` semantics when `color` is a list — likely ignored with a warning.
Relation to #321
#321 conflates two asks under "plotting multiple genes":
- Multi-panel grid for several genes — declined; possibly hosted in a future Squidpy 2.0 wrapper.
- Single-axis additive blend for co-expression visualization — this issue.
The documentation sub-tasks in #321 (`save`, `ncols` on `pl.show()`) are already resolved.
贡献指南
从这里开始
- 先读完整个 Issue,再读项目的贡献指南。
- 在 Issue 下留言说明你要接手 —— 这能避免两个人做同样的事。
- Fork 仓库,在一个分支上完成修改。
- 提交 Pull Request,并在描述里引用这个 Issue 编号。
调研方向
从 pl/render.py 开始,阅读现有的 render_images 多通道分支 2A/2B/2C,然后跟踪 render_shapes、render_labels 和 render_points。完成的标准是支持将 2–3 个连续列作为一个轴上的每通道颜色并进行加法混合,同时定义所列出的 palette 长度、混合类型、NaN、归一化和 groups 行为。
由索引模型根据 Issue 内容生成。
评估
- 技术栈
- python
- 领域
- data-visualization
- Issue 类型
- 功能
- 难度
- 5/5
- 预计耗时
- 一周以上
- 活跃度
- 冷清
- 描述清晰度
- 基本清楚
- 新手友好度
- 45/100