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Add colouring by expression example (tables, layers, gene symbols)
New examples/colouring_by_expression.ipynb on the real Visium mouse-brain dataset (squidpy), documenting where render_* reads colour values from: - color= by a gene (from the annotating table's X) - table_layer= to read from a specific matrix (adds a log1p layer, raw vs lognorm) - gene_symbols= to look genes up by symbol when var is ID-indexed - table_name= to choose among multiple annotating tables The dataset ships a single raw table, so the notebook constructs the layer, the gene-ID index, and a second QC table in-notebook to demonstrate each arg. Executed against spatialdata-plot v0.4.1; committed with outputs. Adds the examples gallery card + toctree + thumbnail. Closes Group C of the round-2 doc-coverage analysis.
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examples/colouring_by_expression.ipynb

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examples/index.md

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@@ -24,6 +24,16 @@ Draw regions of interest directly on a `spatialdata-plot` canvas with
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`sdata.pl.annotate(...)` and persist them as a `ShapesModel` element.
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:::
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:::{grid-item-card} Colouring by expression
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:link: /notebooks/examples/colouring_by_expression
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:link-type: doc
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:img-top: /notebooks/_static/img/colouring_by_expression.png
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Point `render_*` at exactly the values you want: choose the table
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(`table_name`), the matrix (`table_layer`, e.g. raw vs log-normalised), and
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look genes up by symbol (`gene_symbols`).
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:::
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::::
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<!-- gallery-cards-end -->
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@@ -33,4 +43,5 @@ Draw regions of interest directly on a `spatialdata-plot` canvas with
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visium_mouse_brain
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interactive_annotate
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colouring_by_expression
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```

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