mantispy.io.read_jump

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mantispy.io.read_jump#

mantispy.io.read_jump(paths, annotate=True, **kwargs)#

Read JUMP plate profiles, optionally joining the annotation.

Parameters:

  • paths (str | Path | Sequence[str | Path]) – One or more {plate}.parquet files in the Cell Painting Gallery layout.

  • annotate (bool (default: True)) – Join the well and compound tables, which map the three metadata columns to a perturbation. Downloads about 14 MB once and caches it.

  • kwargs (Any) – Passed to read_profiles(). on_column_mismatch="intersect" is useful when plates come from different sources.

Return type:

AnnData

Returns:

An AnnData at well resolution. With annotate it carries Metadata_JCP2022, Metadata_Perturbation, Metadata_InChIKey and Metadata_Control.

Notes

JUMP plates from different sources share their feature names but not always the same set of features; pass on_column_mismatch="intersect" when mixing sources.

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