mantispy.pp.annotate_jump

Contents

mantispy.pp.annotate_jump#

mantispy.pp.annotate_jump(adata, kind='compound', copy=False)#

Join the JUMP annotation onto profiles read from the Cell Painting Gallery.

A JUMP plate parquet records only the source, plate and well of a profile. What the well contained is published in a separate repository keyed by Metadata_JCP2022.

Parameters:

  • adata (AnnData) – Well-level JUMP profiles carrying Metadata_Source, Metadata_Plate and Metadata_Well.

  • kind (str (default: 'compound')) – Which annotation to join. "compound" today.

  • copy (bool (default: False)) – Return an annotated copy instead of annotating in place.

Return type:

AnnData | None

Returns:

None, or the annotated copy. Adds Metadata_JCP2022 (the perturbation identifier), Metadata_Perturbation, Metadata_InChIKey and Metadata_Control, which marks JUMP’s DMSO wells.

Notes

Downloads about 14 MB of annotation once and caches it. Wells the annotation does not cover are kept and logged, since an unannotated well is still a measurement.

Contents