pytometry.tools.normalize_logicle#

pytometry.tools.normalize_logicle(adata, t=262144, m=4.5, w=0.5, a=0, copy=False)#

Logicle transformation.

Parameters

  • adata (AnnData) – AnnData object

  • t (float, optional) – parameter for the top of the linear scale. Defaults to 262144.

  • m (float, optional) – parameter for the number of decades the true logarithmic scale approaches at the high end of the scale. Defaults to 4.5.

  • w (float, optional) – parameter for the approximate number of decades in the linear region. Defaults to 0.5.

  • a (float, optional) – parameter for the additional number of negative decades. Defaults to 0.

  • copy (bool, optional) – Return a copy instead of writing to adata. Defaults to False.

Returns

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

Details:

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.

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