Zero-pad proximity score violin plots - #105
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Complete the extracted proximity table so every component has a value for every presented marker pair, filling missing log2_ratio and join_count_z scores with 0. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
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September 4, 2026 15:38
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This reverts commit 4733ed4.
Show every component in the per-marker proximity violin plots, filling scores that were removed by proximity filtering with 0 instead of dropping the component from the marker's violin. Co-authored-by: max.karlsson <max.karlsson@pixelgen.com>
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Description
The per-marker proximity violin plots dropped any cell whose proximity score for that marker was removed by the isotype-background filtering, so each marker's violin was drawn from a different subset of cells. The violins now show every cell for every marker that is plotted, with the filtered-out scores set to 0.
The padding happens in the visualization only.
es_data$proximityis unchanged, so no colocalization pairs are added globally.complete_proximity_scores()collects the components before theonly_selffilter, so a cell is represented even when all of its self-proximity scores were filtered out, and it fillsjoin_count_zas well aslog2_ratio.component_proximity_per_marker()uses that completion in place of filtering to self-comparisons.An earlier commit on this branch completed the proximity table globally during ingestion; that commit is reverted here.
The comparison below uses the package test data, where 22 of 48 cells have a surviving
CD18score:CD18 proximity violins before and after zero-padding
Type of change
How Has This Been Tested?
Ran the full
testthatsuite locally (R 4.6.1, pixelatorR 0.21.0) — no failures. Added an exact-structure test forcomplete_proximity_scores()covering self-pair and all-pair completion, and regenerated the expected plot data forcomponent_proximity_per_marker().lintr::lint_package()reports no lints.PR checklist:
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