mantispy.pl.cell_cycle

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mantispy.pl.cell_cycle#

mantispy.pl.cell_cycle(adata, dna_feature, by='Metadata_Plate', key='Metadata_CellCyclePhase', layer=None)#

Log DNA intensity per group, colored by assigned phase.

Two separated peaks with the phases split between them indicate a working assignment; a single broad distribution indicates a failed one.

Parameters:

  • adata (AnnData) – Single-cell object cell_cycle_phase() has run on.

  • dna_feature (str) – The DNA intensity feature the phases were assigned from.

  • by (str | None (default: 'Metadata_Plate')) – obs column whose groups become panels, or None for a single panel over every row.

  • key (str (default: 'Metadata_CellCyclePhase')) – obs column holding the assigned phase, whose values are matched against PHASE_COLOURS, so a phase named anything else is not drawn.

  • layer (str | None (default: None)) – Layer to read the intensity from, or None for X. Only positive values are drawn, since the plot takes their logarithm.

Return type:

ndarray

Returns:

A (1, n_groups) array of axes sharing an x axis, one panel per group of by, each holding one filled histogram per phase.

Raises:

  • KeyError – obs has no key column, or dna_feature is not one of var_names.

  • ValueError – The object has no layer named layer.

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