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Update getting_started.rst
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Update docs according to latest changes; The syntax `scv.read` no longer
works and needs to be used with Scanpy directly.
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WeilerP committed Oct 1, 2024
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Showing 1 changed file with 4 additions and 3 deletions.
7 changes: 4 additions & 3 deletions docs/source/getting_started.rst
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Expand Up @@ -11,8 +11,9 @@ counting pipeline.

scVelo workflow at a glance
^^^^^^^^^^^^^^^^^^^^^^^^^^^
Import scvelo as::
Import Scanpy and scvelo as::

import scanpy as sc
import scvelo as scv

For beautified visualization you can change the matplotlib settings to our defaults with::
Expand All @@ -23,7 +24,7 @@ Read your data
''''''''''''''
Read your data file (loom, h5ad, csv, ...) using::

adata = scv.read(filename, cache=True)
adata = sc.read(filename, cache=True)

which stores the data matrix (``adata.X``),
annotation of cells / observations (``adata.obs``) and genes / variables (``adata.var``), unstructured annotation such
Expand All @@ -35,7 +36,7 @@ as graphs (``adata.uns``) and additional data layers where spliced and unspliced

If you already have an existing preprocessed adata object you can simply merge the spliced/unspliced counts via::

ldata = scv.read(filename.loom, cache=True)
ldata = sc.read(filename.loom, cache=True)
adata = scv.utils.merge(adata, ldata)

If you do not have a datasets yet, you can still play around using one of the in-built datasets, e.g.::
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