API

Import AutoGeneS as:

import autogenes as ag

Main functions

init(data[, celltype_key, genes_key, …])

Preprocesses input data

optimize([ngen, mode, nfeatures, weights, …])

Runs multi-objective optimizer

plot([objectives, weights, index, close_to])

Plots objective values of solutions

select([weights, close_to, index, copy, …])

Selects a solution

deconvolve(bulk,key = None[, model])

Performs bulk deconvolution

Auxiliary functions

pipeline(data,bulk, **kwargs)

Runs the optimizer, selection and deconvolution using one method

resume()

Resumes an optimization process that has been interrupted

save(filename)

Saves current state to a file

load(filename)

Loads a state from a file

Accessors

adata()

Returns AnnData object

pareto()

Returns the entire solution set

fitness_matrix()

Returns fitness matrix

selection()

Returns the current selection