vmapper package

Submodules

vmapper.color module

vmapper.meta_func module

vmapper.meta_func.add_meta_info(meta_name, meta_data, func, id_set, id_light=False)

vmapper.meta_func.union(inp)

vmapper.vmapper module

class vmapper.vmapper.mapper(data, data_p, num_cube=10, overlap=0.5, clusterer=DBSCAN(eps=3.0, min_samples=1), adaptive=True)

Bases: object

V-Mapper (Resolution of curse of dimensionality in single-cell data analysis). A noise reduction method for single-cell sequencing data.

Parameters:

data (ndarray/anndata of shape (n_samples, n_features)) – Tranceforming single-cell sequencing data matrix (row:cell, culumn:gene/peak).

log_

Running log.

Type:

dict

out_cytoscape(data, sample_name, meta_data, meta_func, out_dir='.', out_file='mapper', fig_title='')

out_cytoscape_V(data, data_vel, sample_name, meta_data, meta_func, out_dir='.', out_file='vmapper', fig_title='', flow_type='mean')

out_cytoscape_light(sample_name, meta_data, meta_func, out_dir='.', out_file='mapper', fig_title='')

out_fig_cube_docomp(out_dir='.', out_file='mapper', fig_title='')

out_graph(data, data_vel, method='PCA', out_file='graph', title='', label=['', ''])

out_graph_graphviz(out_dir='.', out_file='mapper', fig_title='', fig_fmt='png', fig_layout='fdp')

out_graph_graphviz_V(data, data_vel, out_dir='.', out_file='vmapper', fig_title='', fig_fmt='png', fig_layout='fdp')

out_graph_pca(data, out_dir='.', out_file='mapper', fig_title='', fig_fmt='png')

out_graph_pca_V(data, data_vel, out_dir='.', out_file='vmapper', fig_title='', fig_fmt='png')

out_graph_tsne(data, out_dir='.', out_file='mapper', fig_title='', fig_fmt='png')

out_graph_tsne_V(data, data_vel, out_dir='.', out_file='vmapper', fig_title='', fig_fmt='png')

Module contents