mantispy.pp.annotate_jump

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mantispy.pp.annotate_jump#

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

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, or Metadata_JCP2022 as the assembled profiles do.

  • kind (str (default: 'compound')) – Which annotation to join, "compound", "crispr" or "orf".

  • 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_Perturbation_Type and Metadata_Control. For compounds Metadata_Perturbation_Type is "compound", it adds Metadata_InChIKey, and the controls are JUMP’s DMSO wells. For CRISPR and ORF Metadata_Perturbation is the gene symbol, Metadata_Perturbation_Type is the kind, Metadata_Control marks any control well, and it adds Metadata_Gene, Metadata_Control_Type ("negcon", "poscon" or "treatment") and Metadata_ChromosomeArm, the arm the gene sits on.

Notes

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

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