First compiled on: November 25, 2017. Update March 28, 2017.
import scanpy.api as sc
sc.settings.verbosity = 3 # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.settings.set_figure_params(dpi=80) # low dpi (dots per inch) yields small inline figures
sc.logging.print_versions()
scanpy==1.0 anndata==0.5.8 numpy==1.14.1 scipy==1.0.0 pandas==0.22.0 scikit-learn==0.19.1 statsmodels==0.8.0 python-igraph==0.7.1 louvain==0.6.1
Simulating a simple toggleswitch (Gardner et al., Nature 2000).
adata = sc.tl.sim('toggleswitch')
reading params file /Users/alexwolf/_hholtz/01_projects/1512_scanpy/scanpy/scanpy/sim_models/toggleswitch_params.txt reading simulation results ./write/toggleswitch_sim/sim_000041.txt Observation names are not unique. To make them unique, call `.obs_names_make_unique`.
sc.pl.sim(adata)
sc.pp.neighbors(adata, n_neighbors=10)
computing neighbors using data matrix X directly finished (0:00:02.48) --> added to `.uns['neighbors']` 'distances', weighted adjacency matrix 'connectivities', weighted adjacency matrix
sc.tl.draw_graph(adata)
drawing single-cell graph using layout "fr" finished (0:00:00.34) --> added 'X_draw_graph_fr', graph_drawing coordinates (adata.obs)
sc.pl.draw_graph(adata, edges=True, size=4)