API

Import pytometry as

import pytometry as pt

Read/write (io)

io.read_fcs(path[, reindex])	Read FCS file and convert into AnnData format.
io.read_and_merge(files[, sample_ids, ...])	Read and merge multiple FCS files into a single AnnData object.

Preprocessing (pp)

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

Tools

tl.normalize_arcsinh(adata[, cofactor, inplace])	Inverse hyperbolic sine transformation.
tl.normalize_logicle(adata[, t, m, w, a, ...])	Logicle transformation.
tl.normalize_biexp(adata[, negative, width, ...])	Biexponential transformation.
tl.normalize_autologicle(adata[, channels, ...])	Autologicle transformation.

Plotting

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