API

Flow & mass cytometry analytics.

Import the package:

import pytometry

This is the complete API reference:

Read/write (io)

read_write.read_fcs(path[, reindex])

Read FCS file and convert into AnnData format.

Preprocessing (pp)

preprocessing.split_signal(adata[, var_key, ...])	Method to filter out height or area data.
preprocessing.compensate(adata[, ...])	Computes compensation for data channels.
preprocessing.create_comp_mat(spillmat[, ...])	Creates a compensation matrix from a spillover matrix.
preprocessing.find_indexes(adata[, var_key, ...])	Find channels of interest for computing compensation.

Tools (tl)

tools.normalize_arcsinh(adata, cofactor[, ...])	Inverse hyperbolic sine transformation.
tools.normalize_logicle(adata[, t, m, w, a, ...])	Logicle transformation.
tools.normalize_biExp(adata[, negative, ...])	Biexponential transformation.

Plotting (pl)

plotting.plotdata(adata[, key, normalize, ...])	Creating histogram plot from Anndata object.
plotting.scatter_density(adata[, x, y, ...])	Plots the cell density across two adata.obs.

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Preprocess flow data

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pytometry.read_write.read_fcs