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" or "crispr".

  • 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 Metadata_Perturbation is the gene symbol, Metadata_Perturbation_Type is "crispr", the controls are the no-guide and non-targeting wells, and it adds Metadata_Gene, Metadata_Control_Type ("negcon", "poscon" or "trt") and Metadata_ChromosomeArm, the arm the gene sits on.

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.

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