mantispy.io.read_jump#

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

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 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_Perturbation_Type ("compound"), Metadata_InChIKey and Metadata_Control.