pytometry.tl.normalize_logicle

pytometry.tl.normalize_logicle#

pytometry.tl.normalize_logicle(adata, t=262144, m=4.5, w=0.5, a=0, inplace=True)#

Logicle transformation.

Logicle transformation, implemented as defined in the GatingML 2.0 specification, adapted from FlowKit and Flowutils Python packages.

logicle(x, T, W, M, A) = root(B(y, T, W, M, A) - x)

where B is a modified bi-exponential function defined as

B(y, T, W, M, A) = ae^(by) - ce^(-dy) - f

The Logicle transformation was originally defined in the publication of

Moore WA and Parks DR. Update for the logicle data scale including operational code implementations. Cytometry A., 2012:81A(4):273-277.

Parameters:

  • adata (AnnData) – AnnData object.

  • t (int (default: 262144)) – Parameter for the top of the linear scale.

  • m (float (default: 4.5)) – Parameter for the number of decades the true logarithmic scale approaches at the high end of the scale.

  • w (float (default: 0.5)) – Parameter for the approximate number of decades in the linear region.

  • a (float (default: 0)) – Parameter for the additional number of negative decades.

  • copy – Return a inplace instead of writing to adata.

Return type:

AnnData | None

Returns:

Depending on inplace, returns or updates adata in the following field adata.X is then a normalised adata object

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