mantispy.pp.annotate_jump#

mantispy.pp.annotate_jump(adata, kind='compound', on_unmapped='warn', 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".

on_unmapped str (default: 'warn')

What to do with wells whose id the annotation cannot map: "warn" keeps them, "drop" removes them and warns, "error" raises.

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.