From 446eeb0219e89e0b63a3b04424d70f075babbd3f Mon Sep 17 00:00:00 2001 From: Parashar Date: Tue, 13 Sep 2022 23:01:25 +0200 Subject: [PATCH] updated vignettes --- docs/source/vignettes/cell_subsampling_tutorial.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/docs/source/vignettes/cell_subsampling_tutorial.md b/docs/source/vignettes/cell_subsampling_tutorial.md index ae03f99..60694d5 100644 --- a/docs/source/vignettes/cell_subsampling_tutorial.md +++ b/docs/source/vignettes/cell_subsampling_tutorial.md @@ -114,6 +114,10 @@ ds.plot_layout( --- ### 5) Exporting downsampled data ++++ + +TopACeDo only marks the cells the representative that for downsampling. To create a new subsampled datasets, `SubsetZarr` writer class must be used. This will create a new Zarr file containing only the subset of cells. + ```{code-cell} ipython3 writer = scarf.SubsetZarr( in_zarr='scarf_datasets/tenx_5K_pbmc_rnaseq/data.zarr', @@ -124,6 +128,8 @@ writer = scarf.SubsetZarr( writer.dump() ``` +The downsampled dataset can be loaded as a new DataStore + ```{code-cell} ipython3 ds2 = scarf.DataStore('scarf_datasets/tenx_5K_pbmc_rnaseq/subset.zarr') ``` @@ -132,6 +138,8 @@ ds2 = scarf.DataStore('scarf_datasets/tenx_5K_pbmc_rnaseq/subset.zarr') ds2 ``` +It is expected the downsampled dataset will be small enough to fit in memory. Here the data is exported to anndata format from where it could easily used to perform any downstream analysis from the [scverse](https://scverse.org/) ecosystem. + ```{code-cell} ipython3 adata = ds2.to_anndata() ```