docs: add colouring by expression example (tables, layers, gene symbols) - #24
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timtreis wants to merge 3 commits into
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docs: add colouring by expression example (tables, layers, gene symbols)#24timtreis wants to merge 3 commits into
timtreis wants to merge 3 commits into
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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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📖 Docs preview: https://scverse.org/spatialdata-plot-tutorials/pr-24/gallery.html Built from a5198a4; redeployed on every push. |
…rom throwaway SpatialData (non-destructive), define region keys, table_layer gene-only
…g gene_ids assumption
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Summary
Adds
examples/colouring_by_expression.ipynbdocumenting whererender_*reads colour values from —table_name,table_layer, andgene_symbols(Group C of the round-2 gap analysis; all previously undocumented). Real 10x Visium mouse-brain dataset (squidpy.datasets.visium_hne_sdata()).Covers:
color=by a gene (from the annotating table'sX)table_layer=to read from a specific matrix — adds alog1player and compares raw vslognormgene_symbols=to look genes up by symbol whenvaris ID-indexedtable_name=to choose among multiple annotating tablesThe dataset ships a single raw table, so the notebook constructs the extra layer, the gene-ID index, and a second QC table in-notebook (clearly flagged) to demonstrate each argument — real datasets often already carry them.
Executed against spatialdata-plot v0.4.1, committed with outputs. Adds the examples gallery card + toctree + thumbnail.