mantispy.tl.dna_content#

mantispy.tl.dna_content(adata, dna_feature=None, by=('Metadata_Plate', 'Metadata_Well'), layer=None, min_cells=50, reference=None, key_added='Metadata_DNAContent', copy=False)[source]#

DNA content of each cell, in doublings of the G1 peak of its group.

The integrated DNA intensity is log2-transformed, and the G1 (2N) peak of each by group is subtracted. A cell with a 2N genome then sits near 0 and a cell with a 4N genome near 1, whatever the staining intensity of its well.

Parameters:
adata AnnData

Single-cell object holding raw, unnormalized intensities.

dna_feature str | None (default: None)

The integrated DNA intensity feature. Found when omitted as an integrated intensity, not its edge, whose name or var["channel"] names DNA, DAPI or Hoechst, the Nuclei_ one first.

by Sequence[str] | str | None (default: ('Metadata_Plate', 'Metadata_Well'))

Find the G1 peak separately within each group, normally the well, since staining intensity does not carry across wells.

layer str | None (default: None)

Read this layer instead of X, for example "raw" after normalize(keep_raw=True).

min_cells int (default: 50)

A group with fewer usable cells than this, or fewer reference cells when given, gets no G1 peak, and its cells get NaN.

reference str | None (default: None)

Find each group’s G1 peak on these cells only, and apply it to every cell of the group: "negcon" for the negative controls, or the name of a boolean obs column. None uses every cell. Pass it when a treatment can arrest whole wells, so their peak is not taken for G1; by must then group treated and control cells together, normally by plate, or by well in a pooled screen.

key_added str (default: 'Metadata_DNAContent')

obs column written.

copy bool (default: False)

Return a modified copy instead of mutating in place.

Return type:

AnnData | None

Returns:

None, or the modified copy. Writes obs[key_added], and uns["mantispy"]["dna_content"] with one row per group: the by columns, n_cells (the usable cells the peak was found on) and g1_peak (log2 of the integrated intensity at the G1 peak, NaN for a group below min_cells).

Raises:

  • KeyError – dna_feature was not given and no integrated DNA intensity feature could be found.

  • ValueError – More than 5% of the feature’s values are not positive, so their log cannot be taken.

Notes

The G1 peak is the highest peak of a Gaussian kernel density estimate of the group’s log2 intensities. In a population mostly in G2, such as a well arrested in mitosis, the highest peak is the 4N one. So when a second peak lies one doubling below the highest, within a quarter of a doubling, and is at least a tenth as high, that lower peak is taken as G1. A sub-G1 peak of fragmented nuclei at half the G1 intensity would be mistaken for G1 by the same rule; check g1_peak across wells.

The intensity is used as measured. CellProfiler’s integrated intensity carries no background subtraction, so a strong background lowers the ratio between the 4N and 2N peaks below two. Subtract it before calling this if your pipeline measured it.

A cell whose intensity is missing, zero or negative gets NaN, as does every cell of a group below min_cells.

A stain that does not resolve a 4N peak from the 2N one gives a single broad peak, and its mode is not a G1 peak. The content then still ranks cells by DNA, but dna_state() gates do not mean 2N, S and 4N; look at the histogram first.