2_compute_velocity.md

jupyter	jupytext kernelspec formats text_representation ipynb,md extension format_name format_version jupytext_version .md markdown 1.1 1.2.4 display_name language name (Fertig) Python 3.7 python fertig_python_3_7

from IPython.core.display import display, HTML
display(HTML("<style>.container { width:90% !important; }</style>"))
%matplotlib inline

import scanpy as sc
import scvelo as scv
scv.logging.print_version()

scv.settings.verbosity = 3  # show errors(0), warnings(1), info(2), hints(3)
scv.settings.set_figure_params('scvelo')  # for beautified visualization

adata = scv.read('processed_adata.h5ad')
scv.utils.show_proportions(adata)
adata

https://scvelo-notebooks.readthedocs.io/DentateGyrus.html

scv.pp.filter_and_normalize(adata, min_shared_counts=30, n_top_genes=2000)
scv.pp.moments(adata, n_pcs=30, n_neighbors=30)

adata

scv.tl.velocity(adata)

scv.tl.velocity_graph(adata)
adata

sc.tl.umap(adata)

adata.write_h5ad('adataWithVelocity.h5ad')

scv.pl.velocity_embedding_stream(adata, basis='umap')